Code for zoo data for Female contraception and male castration increase lifespan across vertebrates

Supplmentary Information 1

Author

Michael Garratt, Malgorzata Lagisz, Johanna Stärk, Christine Neyt, Michael Stout, José V. V. Isola, Veronica Cowl, Nannette Driver-Ruiz, Ashley D. Franklin, Monica M. McDonald, David Powell, Susan L. Walker, Jean-Michel Gaillard, Dalia A. Conde, Jean-François Lemaître, Fernando Colchero and Shinichi Nakagawa

Published

December 15, 2023

1 Setting up

1.1 Loading packages

Code
# loading
pacman::p_load(tidyverse,
               metafor,
               pander,
               knitr,
               stringr,
               ape,
               here,
               kableExtra,
               patchwork,
               lme4,
               readxl,
               #metaAidR,
               rotl,
               orchaRd,
               emmeans,
               clubSandwich,
               png,
               grid,
               here,
               cowplot,
               apextra,
               ggimage,
               ggstance,
               ggtree,
)

1.2 Loading data

Code
# main data
dat0 <- read_csv(here("data", "zoo", "zoo.csv"), na = c("", "NA"))

# phylogeny
tree <- read.tree(here("data", "zoo", "tree_zoo.tre"))

# taxonomy
tax <- read.csv(here("data", "zoo", "vertlife_taxonomy_translation_table.csv"))

dat0 %>% left_join(tax, by = c("species" = "zims.species")) -> dat_full

# talking out species with no data (Pseudocheirus peregrinus = likely to be mistaks in data)
dat_full %>% filter(species != "Chrysocyon brachyurus" &
                    species != "Crocuta crocuta" &
                    species != "Neofelis nebulosa" &
                    species != "Panthera uncia" &
                    species != "Pseudocheirus peregrinus") %>% 
  mutate(phylogeny = gsub(" ", "_", vertlife.species)) -> dat

# adding Cervus canadensis
dat$vertlife.species[which(dat$species == "Cervus canadensis")] <-"Cervus canadensis"
dat$phylogeny[which(dat$species == "Cervus canadensis")] <-"Cervus_canadensis"

# fixing species name
dat$species[dat$species == "Equus asinus"] <- "Equus_africanus"
dat$species[dat$species == "Aonyx cinereus"] <- "Aonyx cinerea"
dat$species[dat$species == "Bubalus bubalis"] <- "Bubalus arnee"


# life span data 
to_drop <-
  tree$tip.label[which(!(tree$tip.label %in% unique(dat$phylogeny)))]

tree <- drop.tip(tree, to_drop)

# checking the number of spp
#length(tree$tip.label)

tree <- as.ultrametric(tree)

#tree <- compute.brlen(tree)
cor_tree <- vcv(tree, corr = TRUE)

# length(unique(dat$species))
# length(unique(dat$phylogeny))
# 
# match(unique(gsub(" ","_", dat$species)), unique(dat$phylogeny))
# match(unique(dat$phylogeny), unique(gsub(" ","_", dat$species)))

#write_csv(dat, here("data", "zoo", "original.csv"))

# pre- and post-2005 data for sensitivity analysis
dat_pre <-  read.csv(here("data", "zoo", "hormTabPre05.csv"))
dat_post <-  read.csv(here("data", "zoo","hormTabPost05.csv"))

dat_pre %>% left_join(tax, by = c("species" = "zims.species")) -> dat_pre
dat_post %>% left_join(tax, by = c("species" = "zims.species")) -> dat_post

dat_pre  %>% 
  transmute(F_normal_m = LifeExpNocontMean,
            F_normal_sd = sqrt(Nnocon)*LifeExpNocontSE,
            F_normal_n = Nnocon,
            F_hormonal_m = LifeExpHormMean,
            F_hormonal_sd = sqrt(Nhorm)*LifeExpHormSE,
            F_hormonal_n = Nhorm,
            species = species,
            #species_tree = vertlife.species,
            phylogeny = gsub(" ", "_", vertlife.species)
  ) -> dat_pre

dat_post %>% 
  transmute(F_normal_m = LifeExpNocontMean,
          F_normal_sd = sqrt(Nnocon)*LifeExpNocontSE,
          F_normal_n = Nnocon,
          F_hormonal_m = LifeExpHormMean,
          F_hormonal_sd = sqrt(Nhorm)*LifeExpHormSE,
          F_hormonal_n = Nhorm,
          species = species,
          #species_tree = vertlife.species,
          phylogeny = gsub(" ", "_", vertlife.species)
) -> dat_post

1.3 Custom functions

We have 7 custom functions named : cont_gen(),get_pred1(), get_pred2(), mr_results(), all_models(),folded_mu, and folded_v, all of which are used later and the code is included here.

Code
# custom functions

#' Title: Contrast name generator
#'
#' @param name: a vector of character strings
cont_gen <- function(name) {
  combination <- combn(name, 2)
  name_dat <- t(combination)
  names <- paste(name_dat[, 1], name_dat[, 2], sep = "-")
  return(names)
}

#' @title get_pred1: intercept-less model
#' @description Function to get CIs (confidence intervals) and PIs (prediction intervals) from rma objects (metafor)
#' @param model: rma.mv object 
#' @param mod: the name of a moderator 
get_pred1 <- function (model, mod = " ") {
  name <- firstup(as.character(stringr::str_replace(row.names(model$beta), mod, "")))
  len <- length(name)
  
   if (len != 1) {
        newdata <- diag(len)
        pred <- metafor::predict.rma(model, 
                                     newmods = newdata,
                                     tau2.levels = 1:len)
    }
    else {
        pred <- metafor::predict.rma(model)
  }
  estimate <- pred$pred
  lowerCL <- pred$ci.lb
  upperCL <- pred$ci.ub 
  lowerPR <- pred$cr.lb
  upperPR <- pred$cr.ub 
  
  table <- tibble(name = factor(name, levels = name, labels = name), estimate = estimate,
                  lowerCL = lowerCL, upperCL = upperCL,
                  pval = model$pval,
                  lowerPR = lowerPR, upperPR = upperPR)
}

#' @title get_pred2: normal model
#' @description Function to get CIs (confidence intervals) and PIs (prediction intervals) from rma objects (metafor)
#' @param model: rma.mv object 
#' @param mod: the name of a moderator 
get_pred2 <- function (model, mod = " ") {
  name <- as.factor(str_replace(row.names(model$beta), 
                                paste0("relevel", "\\(", mod,", ref = name","\\)"),""))
  len <- length(name)
  
  if(len != 1){
  newdata <- diag(len)
  pred <- predict.rma(model, intercept = FALSE, newmods = newdata[ ,-1])
  }
  else {
    pred <- predict.rma(model)
  }
  estimate <- pred$pred
  lowerCL <- pred$ci.lb
  upperCL <- pred$ci.ub 
  lowerPR <- pred$cr.lb
  upperPR <- pred$cr.ub 
  
  table <- tibble(name = factor(name, levels = name, labels = name), estimate = estimate,
                  lowerCL = lowerCL, upperCL = upperCL,
                  pval = model$pval,
                  lowerPR = lowerPR, upperPR = upperPR)
}

#' @title mr_results
#' @description Function to put results of meta-regression and its contrasts
#' @param res1: data frame 1
#' @param res1: data frame 2
mr_results <- function(res1, res2) {
  restuls <-tibble(
    `Fixed effect` = c(as.character(res1$name), cont_gen(res1$name)),
    Estimate = c(res1$estimate, res2$estimate),
    `Lower CI [0.025]` = c(res1$lowerCL, res2$lowerCL),
    `Upper CI  [0.975]` = c(res1$upperCL, res2$upperCL),
    `P value` = c(res1$pval, res2$pval),
    `Lower PI [0.025]` = c(res1$lowerPR, res2$lowerPR),
    `Upper PI  [0.975]` = c(res1$upperPR, res2$upperPR),
  )
}


#' @title all_models
#' @description Function to take all possible models and get their results
#' @param model: intercept-less model
#' @param mod: the name of a moderator 

all_models <- function(model, mod = " ", type = "homo") {
  
  # getting the level names out
  level_names <- levels(factor(model$data[[mod]]))
  dat2 <- model$data
  mod <- mod


  run_rma1 <- function(name) {
      VCV1 <- vcalc(vi = dat2$vi,
             cluster = dat2$species,
             rho = 0.5)
      
    rma.mv(yi, V = VCV1,
                   mods = ~relevel(dat2[[mod]], ref = name),
                     random = list(
                       ~1|species,
                       ~1|phylogeny,
                       ~1|obs_id),
                     R = list(phylogeny = cor_tree),
                     data = dat2,
                     control = list(optimizer = "Nelder-Mead"))
   }

    run_rma2 <- function(name) {
    
            VCVa <- vcalc(abs_vi, species, 
                    rho = 0.5, data = dat2)
               
               rma.mv(abs_yi, V = VCVa,
               mods = ~relevel(dat2[[mod]], ref = name),
                     random = list(
                       ~1|species,
                       ~1|phylogeny,
                       ~1|obs_id),
                     R = list(phylogeny = cor_tree),
                     data = dat2,
                     control = list(optimizer = "Nelder-Mead"))
   }

# results of meta-regression including all contrast results; taking the last level out ([-length(level_names)])
# this does not work for hetero model?
if (type == "homo"){

    model_all <- purrr::map(level_names[-length(level_names)], run_rma1)

  } else {
  model_all <- purrr::map(level_names[-length(level_names)], run_rma2)
  }
  
  # getting estimates from intercept-less models (means for all the groups)
  res1 <- get_pred1(model, mod = mod)
  
  # getting estiamtes from all contrast models
  res2_pre <- purrr::map(model_all, ~ get_pred2(.x, mod = mod))
  
  # a list of the numbers to take out unnecessary contrasts
  contra_list <- Map(seq, from=1, to=1:(length(level_names) - 1))
  res2 <- purrr::map2_dfr(res2_pre, contra_list, ~.x[-(.y), ]) 
  # creating a table
  res_tab <- mr_results(res1, res2) %>% 
  kable("html",  digits = 3) %>%
  kable_styling("striped", position = "left") %>%
  scroll_box(width = "100%")
  
  # results
  res_tab

}


##########
# functions for absolute values


# folded mean
folded_mu <-function(mean, variance){
  mu <- mean
  sigma <- sqrt(variance)
  fold_mu <- sigma*sqrt(2/pi)*exp((-mu^2)/(2*sigma^2)) + mu*(1 - 2*pnorm(-mu/sigma))
  fold_mu
} 

# folded variance
folded_v <-function(mean, variance){
  mu <- mean
  sigma <- sqrt(variance)
  fold_mu <- sigma*sqrt(2/pi)*exp((-mu^2)/(2*sigma^2)) + mu*(1 - 2*pnorm(-mu/sigma))
  fold_se <- sqrt(mu^2 + sigma^2 - fold_mu^2)
  # adding se to make bigger mean
  fold_v <-fold_se^2
  fold_v
} 

1.4 Preparing data set (calulating effect sizes)

1.4.1 Comparing contraception vs. normal

Code
##############################################
# data sets comparing normal vs. contraception 
##############################################

# male surgical

dat_m_surg <- dat %>% filter(is.na(Male_Surgical_Mean) == FALSE, is.na(Male_None_Mean) == FALSE) %>% 
  mutate(M_control_m = Male_None_Mean,
         M_control_sd = sqrt(Male.None)*Male_None_SE,
         M_control_n = Male.None,
         M_surgical_m = Male_Surgical_Mean,
         M_surgical_sd = sqrt(Male.Surgical)*Male_Surgical_SE,
         M_surgical_n = Male.Surgical,
         sex = "male",
         type = "surgical")

dat_m_surg <- escalc("ROM", 
              m1i = M_surgical_m,
              m2i = M_control_m,
              sd1i = M_surgical_sd,
              sd2i = M_control_sd,
              n1i = M_surgical_n,
              n2i = M_control_n,
              data = dat_m_surg,
              )

#  male hormonal
dat_m_horm <- dat %>% filter(is.na(Male_Hormonal_Mean) == FALSE, is.na(Male_None_Mean) == FALSE) %>% 
  mutate(M_control_m = Male_None_Mean,
         M_control_sd = sqrt(Male.None)*Male_None_SE,
         M_control_n = Male.None,
         M_hormonal_m = Male_Hormonal_Mean,
         M_hormonal_sd = sqrt(Male.Hormonal)*Male_Hormonal_SE,
         M_hormonal_n = Male.Hormonal,
         sex = "male",
         type = "hormonal")

dat_m_horm <- escalc("ROM", 
                     m1i = M_hormonal_m,
                     m2i = M_control_m,
                     sd1i = M_hormonal_sd,
                     sd2i = M_control_sd,
                     n1i = M_hormonal_n,
                     n2i = M_control_n,
                     data = dat_m_horm,
)

# male immunological
dat_m_immu <- dat %>% filter(is.na(Male_Immunological_Mean) == FALSE, 
    is.na(Male_None_Mean) == FALSE) %>%
  mutate(M_control_m = Male_None_Mean,
         M_control_sd = sqrt(Male.None)*Male_None_SE,
         M_control_n = Male.None,
         M_immunol_m = Male_Immunological_Mean,
         M_immunol_sd = sqrt(Male.Immunological)*Male_Immunological_SE,
         M_immunol_n = Male.Immunological,
         sex = "male",
         type = "immunological")

dat_m_immu <- escalc("ROM", 
                     m1i = M_immunol_m,
                     m2i = M_control_m,
                     sd1i = M_immunol_sd,
                     sd2i = M_control_sd,
                     n1i = M_immunol_n,
                     n2i = M_control_n,
                     data = dat_m_immu,
)


# female hormonal data 

dat_f_horm <- dat %>% filter(is.na(Female_Hormonal_Mean) == FALSE, is.na(Female_None_Mean) == FALSE) %>% 
  mutate(F_control_m = Female_None_Mean,
         F_control_sd = sqrt(Female.None)*Female_None_SE,
         F_control_n = Female.None,
         F_hormonal_m = Female_Hormonal_Mean,
         F_hormonal_sd = sqrt(Female.Hormonal)*Female_Hormonal_SE,
         F_hormonal_n = Female.Hormonal,
         sex = "female",
         type = "hormonal")

dat_f_horm <- escalc("ROM", 
                     m1i = F_hormonal_m,
                     m2i = F_control_m,
                     sd1i = F_hormonal_sd,
                     sd2i = F_control_sd,
                     n1i = F_hormonal_n,
                     n2i = F_control_n,
                     data = dat_f_horm,
)

# female surgical data

dat_f_surg<- dat %>% filter(is.na(Female_Surgical_Mean) == FALSE, is.na(Female_None_Mean) == FALSE) %>% 
  mutate(F_control_m = Female_None_Mean,
         F_control_sd = sqrt(Female.None)*Female_None_SE,
         F_control_n = Female.None,
         F_surgical_m = Female_Surgical_Mean,
         F_surgical_sd = sqrt(Female.Surgical)*Female_Surgical_SE,
         F_surgical_n = Female.Surgical,
         sex = "female",
         type = "surgical")


dat_f_surg <- escalc("ROM", 
                     m1i = F_surgical_m,
                     m2i = F_control_m,
                     sd1i = F_surgical_sd,
                     sd2i = F_control_sd,
                     n1i = F_surgical_n,
                     n2i = F_control_n,
                     data = dat_f_surg,
)

# female immunological
dat_f_immu <- dat %>% filter(is.na(Female_Immunological_Mean) == FALSE, 
    is.na(Female_None_Mean) == FALSE) %>%
  mutate(F_control_m = Female_None_Mean,
         F_control_sd = sqrt(Female.None)*Female_None_SE,
         F_control_n = Female.None,
         F_immunol_m = Female_Immunological_Mean,
         F_immunol_sd = sqrt(Female.Immunological)*Female_Immunological_SE,
         F_immunol_n = Female.Immunological,
         sex = "female",
         type = "immunological")

dat_f_immu <- escalc("ROM", 
                     m1i = F_immunol_m,
                     m2i = F_control_m,
                     sd1i = F_immunol_sd,
                     sd2i = F_control_sd,
                     n1i = F_immunol_n,
                     n2i = F_control_n,
                     data = dat_f_immu,
)


rbind(
dat_m_horm[ , c(1, 53, 55, 62:65)], # 1
dat_m_surg[ , c(1, 53, 55, 62:65)], # 2
dat_f_horm[ , c(1, 53, 55, 62:65)], # 3 
dat_f_surg[ , c(1, 53, 55, 62:65)], # 4
dat_m_immu[ , c(1, 53, 55, 62:65)], # 5
dat_f_immu[ , c(1, 53, 55, 62:65)] # 6
) -> dat_all

# observation id
dat_all$obs_id <- factor(1:nrow(dat_all))

# sex type combined
dat_all %>% mutate(sex_type = paste(sex, type, sep = "_")) -> dat_all

#write_csv(dat_all, here("data", "zoo", "effect1.csv"))

1.4.2 Examining sex differences

Code
######################################
# data sets looking at sex differences
######################################

# female normal vs. male surgical (1)

dat_fm_ns <- dat %>% filter(is.na(Female_None_Mean) == FALSE, 
                            is.na(Male_Surgical_Mean) == FALSE) %>% 
  transmute(F_normal_m = Male_None_Mean,
         F_normal_sd = sqrt(Female.None)*Female_None_SE,
         F_normal_n = Female.None,
         M_surgical_m = Male_Surgical_Mean,
         M_surgical_sd = sqrt(Male.Surgical)*Male_Surgical_SE,
         M_surgical_n = Male.Surgical,
         species = species,
         phylogeny = phylogeny,
         category = "F normal/M surgical"
         )

dat_fm_ns <- escalc("ROM", 
              m1i = F_normal_m,
              m2i = M_surgical_m,
              sd1i = F_normal_sd,
              sd2i = M_surgical_sd,
              n1i = F_normal_n,
              n2i = M_surgical_n,
              data = dat_fm_ns,
              )

# female hormonal vs. male normal (2)

dat_fm_hn <- dat %>% filter(is.na(Female_Hormonal_Mean) == FALSE, 
                            is.na(Male_None_Mean) == FALSE) %>% 
  transmute(F_hormonal_m = Female_Hormonal_Mean,
         F_hormonal_sd = sqrt(Female.Hormonal*Female_Hormonal_SE),
         F_hormonal_n = Female.Hormonal,
         M_normal_m = Male_None_Mean,
         M_normal_sd = sqrt(Male.None)*Male_None_SE,
         M_normal_n = Male.None,
         species = species,
         phylogeny = phylogeny,
         category = "F hormonal/M normal"
         )

dat_fm_hn <- escalc("ROM", 
              m1i = F_hormonal_m,
              m2i = M_normal_m,
              sd1i = F_hormonal_sd,
              sd2i = M_normal_sd,
              n1i = F_hormonal_n,
              n2i = M_normal_m,
              data = dat_fm_hn,
              )



# female surgical vs. male normal (3)

dat_fm_sn <- dat %>% filter(is.na(Female_Surgical_Mean) == FALSE,
                            is.na(Male_None_Mean) == FALSE) %>%
  transmute(F_surgical_m = Female_Surgical_Mean,
         F_surgical_sd = sqrt(Female.Surgical*Female_Surgical_SE),
         F_surgical_n = Female.Surgical,
         M_normal_m = Male_None_Mean,
         M_normal_sd = sqrt(Male.None)*Male_None_SE,
         M_normal_n = Male.None,
         species = species,
         phylogeny = phylogeny,
         category = "F hormonal/M normal"
         )

dat_fm_sn <- escalc("ROM", 
              m1i = F_surgical_m,
              m2i = M_normal_m,
              sd1i = F_surgical_sd,
              sd2i = M_normal_sd,
              n1i = F_surgical_n,
              n2i = M_normal_n,
              data = dat_fm_sn,
              )


# female surgical vs. male surgical (4)

dat_fm_ss <- dat %>% filter(is.na(Female_Surgical_Mean) == FALSE, 
                            is.na(Male_Surgical_Mean) == FALSE) %>% 
    transmute(F_surgical_m = Female_Surgical_Mean,
                 F_surgical_sd = sqrt(Female.Surgical*Female_Surgical_SE),
                 F_surgical_n = Female.Surgical,
                 M_surgical_m = Male_Surgical_Mean,
                 M_surgical_sd = sqrt(Male.Surgical)*Male_Surgical_SE,
                 M_surgical_n = Male.Surgical,
                 species = species,
                 phylogeny = phylogeny,
                 category = "F surgical/M surgical"
                 )

dat_fm_ss <- escalc("ROM", 
                            m1i = F_surgical_m,
                            m2i = M_surgical_m,
                            sd1i = F_surgical_sd,
                            sd2i = M_surgical_sd,
                            n1i = F_surgical_n,
                            n2i = M_surgical_n,
                            data = dat_fm_ss,
                            )

# female normal vs. male normal (5)

dat_fm_nn <- dat %>% filter(is.na(Female_None_Mean) == FALSE, 
                                                        is.na(Male_None_Mean) == FALSE) %>% 
    transmute(F_normal_m = Female_None_Mean,
                 F_normal_sd = sqrt(Female.None*Female_None_SE),
                 F_normal_n = Female.None,
                 M_normal_m = Male_None_Mean,
                 M_normal_sd = sqrt(Male.None*Male_None_SE),
                 M_normal_n = Male.None,
                 species = species,
                 phylogeny = phylogeny,
                 category = "F normal/M normal"
                 )

dat_fm_nn <- escalc("ROM", 
                            m1i = F_normal_m,
                            m2i = M_normal_m,
                            sd1i = F_normal_sd,
                            sd2i = M_normal_sd,
                            n1i = F_normal_n,
                            n2i = M_normal_n,
                            data = dat_fm_nn,
                            )

# female normal vs. male hormonal (6)

dat_fm_nh <- dat %>% filter(is.na(Female_None_Mean) == FALSE,
                            is.na(Male_Hormonal_Mean) == FALSE) %>%
  transmute(F_normal_m = Female_None_Mean,
            F_normal_sd = sqrt(Female.None*Female_None_SE),
            F_normal_n = Female.None,
            M_hornomal_m = Male_Hormonal_Mean,
            M_hornomal_sd = sqrt(Male.Hormonal)*Male_Hormonal_SE,
            M_hornomal_n = Male.Hormonal,
            species = species,
            phylogeny = phylogeny,
            category = "F normal/M hornomal"
  )

dat_fm_nh <- escalc("ROM", 
                    m1i = F_normal_m,
                    m2i = M_hornomal_m,
                    sd1i = F_normal_sd,
                    sd2i = M_hornomal_sd,
                    n1i = F_normal_n,
                    n2i = M_hornomal_n,
                    data = dat_fm_nh,
)

# female normal vs. male immunological (7)

dat_fm_ni <- dat %>% filter(is.na(Female_None_Mean) == FALSE,
                            is.na(Male_Immunological_Mean) == FALSE) %>%
  transmute(F_normal_m = Female_None_Mean,
            F_normal_sd = sqrt(Female.None*Female_None_SE),
            F_normal_n = Female.None,
            M_immunological_m = Male_Immunological_Mean,
            M_immunological_sd = sqrt(Male.Immunological)*Male_Immunological_SE,
            M_immunological_n = Male.Immunological,
            species = species,
            phylogeny = phylogeny,
            category = "F normal/M immunological"
  )
        
dat_fm_ni <- escalc("ROM", 
                    m1i = F_normal_m,
                    m2i = M_immunological_m,
                    sd1i = F_normal_sd,
                    sd2i = M_immunological_sd,
                    n1i = F_normal_n,
                    n2i = M_immunological_n,
                    data = dat_fm_ni,
)

# female immunological vs. male normal (8)

dat_fm_in <- dat %>% filter(is.na(Female_Immunological_Mean) == FALSE,
                            is.na(Male_None_Mean) == FALSE) %>%
  transmute(F_immunological_m = Female_Immunological_Mean,
            F_immunological_sd = sqrt(Female.Immunological*Female_Immunological_SE),
            F_immunological_n = Female.Immunological,
            M_normal_m = Male_None_Mean,
            M_normal_sd = sqrt(Male.None)*Male_None_SE,
            M_normal_n = Male.None,
            species = species,
            phylogeny = phylogeny,
            category = "F immunological/M normal"
  )

dat_fm_in <- escalc("ROM", 
                    m1i = F_immunological_m,
                    m2i = M_normal_m,
                    sd1i = F_immunological_sd,
                    sd2i = M_normal_sd,
                    n1i = F_immunological_n,
                    n2i = M_normal_n,
                    data = dat_fm_in,
)


# female hormonal vs. male hormonal (9)

dat_fm_hh <- dat %>% filter(is.na(Female_Hormonal_Mean) == FALSE,
                            is.na(Male_Hormonal_Mean) == FALSE) %>%
  transmute(F_hornomal_m = Female_Hormonal_Mean,
            F_hornomal_sd = sqrt(Female.Hormonal*Female_Hormonal_SE),
            F_hornomal_n = Female.Hormonal,
            M_hornomal_m = Male_Hormonal_Mean,
            M_hornomal_sd = sqrt(Male.Hormonal)*Male_Hormonal_SE,
            M_hornomal_n = Male.Hormonal,
            species = species,
            phylogeny = phylogeny,
            category = "F hornomal/M hornomal"
  )
     
dat_fm_hh <- escalc("ROM", 
                    m1i = F_hornomal_m,
                    m2i = M_hornomal_m,
                    sd1i = F_hornomal_sd,
                    sd2i = M_hornomal_sd,
                    n1i = F_hornomal_n,
                    n2i = M_hornomal_n,
                    data = dat_fm_hh,
)


# female immunological vs. male immunological (10)

dat_fm_ii <- dat %>% filter(is.na(Female_Immunological_Mean) == FALSE,
                    is.na(Male_Immunological_Mean) == FALSE) %>%
  transmute(F_immunological_m = Female_Immunological_Mean,
            F_immunological_sd = sqrt(Female.Immunological*Female_Immunological_SE),
            F_immunological_n = Female.None,
            M_immunological_m = Male_Immunological_Mean,
            M_immunological_sd = sqrt(Male.Immunological)*Male_Immunological_SE,
            M_immunological_n = Male.Immunological,
            species = species,
            phylogeny = phylogeny,
            category = "F immunological/M immunological"
  )

dat_fm_ii <- escalc("ROM", 
                    m1i = F_immunological_m,
                    m2i = M_immunological_m,
                    sd1i = F_immunological_sd,
                    sd2i = M_immunological_sd,
                    n1i = F_immunological_n,
                    n2i = M_immunological_n,
                    data = dat_fm_ii,
)

rbind(
  dat_fm_ns[ , 7:11], # 1
  dat_fm_hn[ , 7:11], # 2 
  dat_fm_sn[ , 7:11], # 3
  dat_fm_ss[ , 7:11], # 4
  dat_fm_nn[ , 7:11], # 5
  dat_fm_nh[ , 7:11], # 6
  dat_fm_ni[ , 7:11], # 7
  dat_fm_in[ , 7:11], # 8
  dat_fm_hh[ , 7:11], # 9
  dat_fm_ii[ , 7:11]  # 10
) -> dat_comb


dat_comb$obs_id <- factor(1:nrow(dat_comb))

# adding category
dat_comb$contraception <- factor(dat_comb$category, levels = c("F immunological/M immunological",
                                                           "F hornomal/M hornomal",
                                                           "F surgical/M surgical",
                                                           "F immunological/M normal",
                                                           "F hormonal/M normal",  
                                                           "F surgical/M normal",
                                                           "F normal/M immunological",
                                                           "F normal/M hormonal",
                                                           "F normal/M surgical",
                                                           "F normal/M normal"),
                                                labels = c("F contra./M contra.",
                                                           "F contra./M contra.",
                                                           "F contra./M contra.",
                                                           "F contra./M normal",
                                                           "F contra./M normal",  
                                                           "F contra./M normal",
                                                           "F normal/M contra.",
                                                           "F normal/M contra.",
                                                           "F normal/M contra.",
                                                           "F normal/M normal"),
                             
)

# absolute values
dat_comb <- dat_comb %>% mutate(
  abs_yi = abs(yi), # we use this one (conservative)
  abs_yi2 = folded_mu(yi, vi), # alternative way
  abs_vi = folded_v(yi, vi))


#write_csv(dat_comb, here("data", "zoo", "effect2.csv"))

1.4.3 Comparing before and after 2005

Code
# getting effect size

dat_pre <- escalc("ROM", 
                    m2i = F_normal_m,
                    m1i = F_hormonal_m,
                    sd2i = F_normal_sd,
                    sd1i = F_hormonal_sd,
                    n2i = F_normal_n,
                    n1i = F_hormonal_n,
                    data = dat_pre,
)

dat_post <- escalc("ROM", 
                  m2i = F_normal_m,
                  m1i = F_hormonal_m,
                  sd2i = F_normal_sd,
                  sd1i = F_hormonal_sd,
                  n2i = F_normal_n,
                  n1i = F_hormonal_n,
                  data = dat_post,
)

# combining
rbind(
  dat_pre[ , 7:10], # 1
  dat_post[ , 7:10]# 2 
) -> dat_pre_post

# 54 effect sizes and 
# unique(dat_pre_post$species 

dat_pre_post$obs_id <- factor(1:nrow(dat_pre_post))

# adding category
dat_pre_post$timing <- rep(c("Pre-2005","Post-2005"),c(dim(dat_pre)[1], dim(dat_post)[1]))

2 Datasets

Code
kable(dat, "html", escape = FALSE, digits = 3) %>% kable_styling("striped", position = "left", full_width = TRUE) %>% 
  scroll_box(width = "100%", 
    height = "500px")
species Female_None_Mean Female_None_SE Female_None_Lower Female_None_Upper Female_Hormonal_Mean Female_Hormonal_SE Female_Hormonal_Lower Female_Hormonal_Upper Female_Immunological_Mean Female_Immunological_SE Female_Immunological_Lower Female_Immunological_Upper Female_Surgical_Mean Female_Surgical_SE Female_Surgical_Lower Female_Surgical_Upper Female_Undetermined_Mean Female_Undetermined_SE Female_Undetermined_Lower Female_Undetermined_Upper Male_None_Mean Male_None_SE Male_None_Lower Male_None_Upper Male_Hormonal_Mean Male_Hormonal_SE Male_Hormonal_Lower Male_Hormonal_Upper Male_Immunological_Mean Male_Immunological_SE Male_Immunological_Lower Male_Immunological_Upper Male_Surgical_Mean Male_Surgical_SE Male_Surgical_Lower Male_Surgical_Upper Male_Undetermined_Mean Male_Undetermined_SE Male_Undetermined_Lower Male_Undetermined_Upper Female.None Female.Hormonal Female.Immunological Female.Surgical Female.Undetermined Male.None Male.Hormonal Male.Immunological Male.Surgical Male.Undetermined vertlife.species order Note phylogeny
Acinonyx jubatus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9.423 0.116 9.198 9.659 NA NA NA NA NA NA NA NA 9.959 0.884 8.354 11.824 NA NA NA NA 0 0 0 0 0 2948 8 0 38 2 Acinonyx jubatus Carnivora NA Acinonyx_jubatus
Addax nasomaculatus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.744 0.236 7.292 8.220 NA NA NA NA NA NA NA NA 9.173 0.791 7.707 10.840 6.876 0.930 5.221 8.887 0 0 0 0 0 2856 1 2 93 34 Addax nasomaculatus Artiodactyla NA Addax_nasomaculatus
Aepyceros melampus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5.212 0.230 4.784 5.684 NA NA NA NA NA NA NA NA 7.671 0.869 6.168 9.609 NA NA NA NA 0 0 0 0 0 2330 4 2 157 19 Aepyceros melampus Artiodactyla NA Aepyceros_melampus
Ailurus fulgens 9.665 0.194 9.286 10.042 8.196 0.774 6.755 9.787 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1475 66 0 8 10 0 0 0 0 0 Ailurus fulgens Carnivora NA Ailurus_fulgens
Alouatta caraya 12.154 0.722 10.802 13.674 18.966 1.927 15.500 22.913 NA NA NA NA NA NA NA NA 18.400 1.581 15.434 21.744 13.442 0.627 12.275 14.696 NA NA NA NA NA NA NA NA 13.984 2.085 10.349 18.360 NA NA NA NA 292 62 0 12 44 398 8 0 33 5 Alouatta caraya Primates NA Alouatta_caraya
Ammotragus lervia NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9.824 0.184 9.472 10.205 NA NA NA NA NA NA NA NA 10.192 0.732 8.875 11.717 NA NA NA NA 0 0 0 0 0 4879 0 0 162 26 Ammotragus lervia Artiodactyla NA Ammotragus_lervia
Antidorcas marsupialis NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4.448 0.190 4.101 4.841 NA NA NA NA NA NA NA NA 4.036 0.637 2.967 5.455 NA NA NA NA 0 0 0 0 0 1850 5 0 48 22 Antidorcas marsupialis Artiodactyla NA Antidorcas_marsupialis
Antilope cervicapra NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5.595 0.133 5.349 5.861 NA NA NA NA NA NA NA NA 9.470 0.719 8.180 10.987 NA NA NA NA 0 0 0 0 0 6621 0 2 347 10 Antilope cervicapra Artiodactyla NA Antilope_cervicapra
Aonyx cinerea 9.358 0.184 8.992 9.721 11.164 0.978 9.417 13.229 NA NA NA NA NA NA NA NA 7.139 0.918 5.495 9.117 10.799 0.226 10.371 11.248 12.387 1.982 8.959 16.703 NA NA NA NA 11.156 0.858 9.593 12.924 NA NA NA NA 2205 95 0 18 30 2260 42 0 96 19 Aonyx cinerea Carnivora NA Aonyx_cinerea
Arctictis binturong NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 15.016 0.479 14.109 15.969 NA NA NA NA NA NA NA NA 15.660 1.868 12.285 19.610 NA NA NA NA 0 0 0 0 0 636 2 0 30 5 Arctictis binturong Carnivora NA Arctictis_binturong
Artibeus jamaicensis NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5.409 0.326 4.810 6.065 NA NA NA NA NA NA NA NA 9.539 1.336 7.322 12.581 NA NA NA NA 0 0 0 0 0 670 0 0 64 18 Artibeus jamaicensis Chiroptera NA Artibeus_jamaicensis
Ateles fusciceps 26.272 3.043 22.290 34.681 33.642 11.571 19.709 60.738 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 438 32 0 16 13 0 0 0 0 0 Ateles fusciceps Primates NA Ateles_fusciceps
Ateles geoffroyi 23.006 0.791 21.531 24.626 24.663 4.024 17.296 33.214 NA NA NA NA NA NA NA NA NA NA NA NA 25.036 1.343 22.560 27.885 NA NA NA NA NA NA NA NA 23.793 2.631 18.898 29.256 NA NA NA NA 679 32 0 22 21 580 4 2 51 23 Ateles geoffroyi Primates NA Ateles_geoffroyi
Axis axis 12.285 0.318 11.712 12.934 11.212 1.450 8.679 14.356 NA NA NA NA NA NA NA NA NA NA NA NA 15.674 3.727 11.584 25.946 NA NA NA NA NA NA NA NA 8.849 2.104 6.102 14.295 NA NA NA NA 4437 42 0 1 0 3737 0 0 87 11 Axis axis Artiodactyla NA Axis_axis
Bison bison 15.482 0.244 15.009 15.976 NA NA NA NA 19.018 2.762 14.200 25.091 NA NA NA NA NA NA NA NA 12.303 0.335 11.676 12.990 NA NA NA NA NA NA NA NA 12.889 1.000 11.036 15.022 NA NA NA NA 4235 8 33 2 12 3703 0 0 104 18 Bison bison Artiodactyla NA Bison_bison
Bos grunniens NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 10.582 0.459 9.733 11.532 NA NA NA NA NA NA NA NA 11.799 1.912 8.470 15.999 NA NA NA NA 0 0 0 0 0 1374 0 0 37 5 Bos grunniens Artiodactyla NA Bos_grunniens
Bos javanicus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 10.610 0.480 9.751 11.604 NA NA NA NA NA NA NA NA 8.666 1.689 5.895 12.370 NA NA NA NA 0 0 0 0 0 998 2 2 32 3 Bos javanicus Artiodactyla NA Bos_javanicus
Bos taurus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 10.669 0.339 10.013 11.345 NA NA NA NA NA NA NA NA 15.002 1.314 12.579 17.745 14.326 2.577 10.072 20.076 0 0 0 0 0 4303 0 0 271 49 Bos taurus Artiodactyla NA Bos_taurus
Boselaphus tragocamelus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 10.322 0.549 9.294 11.478 NA NA NA NA NA NA NA NA 9.621 1.582 7.014 13.228 NA NA NA NA 0 0 0 0 0 2180 1 2 57 18 Boselaphus tragocamelus Artiodactyla NA Boselaphus_tragocamelus
Bubalus arnee NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 10.109 0.671 8.848 11.498 NA NA NA NA NA NA NA NA 18.191 2.299 13.827 22.791 NA NA NA NA 0 0 0 0 0 622 1 0 36 6 Bubalus arnee Artiodactyla Replaced with wild ancestor (B. arnee is wild ancestor of B. bubalis) Bubalus_arnee
Callimico goeldii 9.430 0.286 8.893 10.004 8.770 1.391 6.398 11.855 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1072 42 0 19 17 0 0 0 0 0 Callimico goeldii Primates NA Callimico_goeldii
Callithrix geoffroyi 6.219 0.221 5.806 6.679 5.803 0.722 4.509 7.337 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1043 65 0 4 17 0 0 0 0 0 Callithrix geoffroyi Primates NA Callithrix_geoffroyi
Callithrix jacchus 6.988 0.184 6.634 7.364 7.428 0.981 5.774 9.580 NA NA NA NA NA NA NA NA NA NA NA NA 7.807 0.175 7.468 8.159 NA NA NA NA NA NA NA NA 11.274 1.428 8.815 14.411 NA NA NA NA 3206 147 0 21 8 3868 12 0 115 6 Callithrix jacchus Primates NA Callithrix_jacchus
Camelus bactrianus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 13.932 0.387 13.207 14.704 NA NA NA NA NA NA NA NA 12.119 1.117 10.091 14.470 NA NA NA NA 0 0 0 0 0 2081 5 1 94 17 Camelus bactrianus Artiodactyla NA Camelus_bactrianus
Camelus dromedarius NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14.626 0.536 13.633 15.707 NA NA NA NA NA NA NA NA 14.997 1.632 12.050 18.458 NA NA NA NA 0 0 0 0 0 1182 0 0 109 10 Camelus dromedarius Artiodactyla NA Camelus_dromedarius
Canis latrans 9.244 0.465 8.319 10.148 NA NA NA NA NA NA NA NA 11.731 1.106 9.658 13.968 NA NA NA NA 8.106 0.458 7.215 9.006 NA NA NA NA NA NA NA NA 11.262 0.919 9.540 13.098 NA NA NA NA 485 4 0 39 7 529 0 0 64 10 Canis latrans Carnivora NA Canis_latrans
Canis lupus 9.907 0.143 9.623 10.186 7.054 0.744 5.763 8.606 NA NA NA NA 10.898 0.524 9.913 11.941 10.938 1.116 8.928 13.303 10.289 0.141 10.019 10.566 NA NA NA NA NA NA NA NA 10.078 0.407 9.315 10.909 10.717 1.191 8.602 13.153 5012 130 0 331 59 5457 28 0 439 58 Canis lupus Carnivora NA Canis_lupus
Capra aegagrus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.630 0.353 6.974 8.354 NA NA NA NA NA NA NA NA 10.343 2.183 6.668 15.305 NA NA NA NA 0 0 0 0 0 1107 0 0 42 0 Capra aegagrus Artiodactyla NA Capra_aegagrus
Capra falconeri NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 6.912 0.244 6.456 7.400 NA NA NA NA NA NA NA NA 7.413 1.119 5.436 9.854 NA NA NA NA 0 0 0 0 0 1948 11 0 43 2 Capra falconeri Artiodactyla NA Capra_falconeri
Capra hircus 9.327 0.067 9.198 9.456 8.427 1.257 6.284 11.241 NA NA NA NA NA NA NA NA NA NA NA NA 9.007 0.118 8.779 9.234 NA NA NA NA NA NA NA NA 9.207 0.199 8.820 9.612 9.295 0.517 8.326 10.332 24855 44 8 25 10 17776 0 22 2384 375 Capra hircus Artiodactyla NA Capra_hircus
Capra nubiana NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.246 0.242 6.786 7.738 NA NA NA NA NA NA NA NA 8.857 1.098 6.930 11.224 NA NA NA NA 0 0 0 0 0 2435 0 0 49 2 Capra nubiana Artiodactyla NA Capra_nubiana
Carollia perspicillata NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4.667 0.218 4.249 5.101 NA NA NA NA NA NA NA NA 12.445 2.567 8.471 18.341 NA NA NA NA 0 0 0 0 0 843 0 0 155 4 Carollia perspicillata Chiroptera NA Carollia_perspicillata
Cavia porcellus 4.345 0.056 4.236 4.458 NA NA NA NA NA NA NA NA 3.409 0.400 2.694 4.265 NA NA NA NA 3.912 0.088 3.743 4.085 NA NA NA NA NA NA NA NA 4.352 0.324 3.746 5.027 NA NA NA NA 3807 2 0 40 0 2057 0 0 151 10 Cavia porcellus Rodentia NA Cavia_porcellus
Cebuella pygmaea 6.348 0.163 6.036 6.680 8.149 1.791 5.380 12.210 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2304 34 0 5 22 0 0 0 0 0 Cebuella pygmaea Primates NA Cebuella_pygmaea
Cebus capucinus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 21.202 3.026 16.744 28.538 NA NA NA NA NA NA NA NA 50.300 27.022 26.667 123.882 NA NA NA NA 0 0 0 0 0 309 1 0 45 4 Cebus capucinus Primates NA Cebus_capucinus
Cercopithecus neglectus 14.432 0.720 13.105 15.898 18.187 4.089 11.356 27.327 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 483 32 0 6 19 0 0 0 0 0 Cercopithecus neglectus Primates NA Cercopithecus_neglectus
Cervus canadensis 13.741 0.262 13.216 14.253 13.870 1.458 11.179 16.851 NA NA NA NA NA NA NA NA NA NA NA NA 9.206 0.327 8.579 9.867 NA NA NA NA NA NA NA NA 14.531 2.120 10.870 19.066 NA NA NA NA 2370 30 19 2 6 2111 1 0 40 12 Cervus canadensis Artiodactyla synonym Cervus_canadensis
Cervus elaphus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8.672 0.368 7.973 9.413 NA NA NA NA NA NA NA NA 7.781 0.853 6.257 9.577 NA NA NA NA 0 0 0 0 0 1825 0 0 55 2 Cervus elaphus Artiodactyla NA Cervus_elaphus
Cervus nippon NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.884 0.262 7.385 8.421 NA NA NA NA NA NA NA NA 6.131 0.945 4.523 8.195 NA NA NA NA 0 0 0 0 0 2975 4 0 70 14 Cervus nippon Artiodactyla NA Cervus_nippon
Chinchilla lanigera NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.234 0.229 6.795 7.700 NA NA NA NA NA NA NA NA 8.095 1.211 5.941 10.827 NA NA NA NA 0 0 0 0 0 1440 0 0 47 3 Chinchilla lanigera Rodentia NA Chinchilla_lanigera
Chlorocebus aethiops NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14.820 0.911 13.225 16.847 NA NA NA NA NA NA NA NA 18.375 4.681 10.978 29.032 NA NA NA NA 0 0 0 0 0 685 1 0 30 3 Chlorocebus aethiops Primates NA Chlorocebus_aethiops
Colobus angolensis 12.650 1.669 9.917 16.476 19.286 6.116 11.799 34.639 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 189 34 0 7 3 0 0 0 0 0 Colobus angolensis Primates NA Colobus_angolensis
Colobus guereza 9.668 0.338 9.021 10.331 15.369 1.508 12.650 18.522 NA NA NA NA NA NA NA NA 12.945 1.249 10.646 15.553 13.940 0.481 13.045 14.908 NA NA NA NA NA NA NA NA 14.185 1.733 11.099 17.936 NA NA NA NA 1174 122 0 24 60 1352 4 0 57 15 Colobus guereza Primates NA Colobus_guereza
Connochaetes taurinus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.445 0.298 6.890 8.051 NA NA NA NA NA NA NA NA 10.543 0.969 8.731 12.558 6.272 1.477 3.808 9.571 0 0 0 0 0 1469 1 1 114 33 Connochaetes taurinus Artiodactyla NA Connochaetes_taurinus
Cynomys ludovicianus 5.678 0.160 5.383 6.005 NA NA NA NA NA NA NA NA 4.675 0.702 3.493 6.227 NA NA NA NA 5.308 0.175 4.985 5.670 NA NA NA NA NA NA NA NA 4.946 0.458 4.123 5.918 NA NA NA NA 2858 7 0 65 6 2465 9 0 154 16 Cynomys ludovicianus Rodentia NA Cynomys_ludovicianus
Dama dama NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.913 0.248 7.455 8.422 NA NA NA NA NA NA NA NA 9.404 1.179 7.351 11.942 4.947 1.006 3.326 7.249 0 0 0 0 0 4616 0 0 173 30 Dama dama Artiodactyla NA Dama_dama
Damaliscus pygargus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 6.227 0.247 5.759 6.715 NA NA NA NA NA NA NA NA 6.734 1.063 4.946 9.091 NA NA NA NA 0 0 0 0 0 1187 1 1 38 15 Damaliscus pygargus Artiodactyla NA Damaliscus_pygargus
Desmodus rotundus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8.052 0.304 7.466 8.663 NA NA NA NA NA NA NA NA 13.507 1.594 10.437 16.778 NA NA NA NA 0 0 0 0 0 933 0 0 66 1 Desmodus rotundus Chiroptera NA Desmodus_rotundus
Didelphis virginiana NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1.469 0.054 1.367 1.576 NA NA NA NA NA NA NA NA 2.279 0.270 1.811 2.883 NA NA NA NA 0 0 0 0 0 1610 0 0 79 7 Didelphis virginiana Didelphimorphia NA Didelphis_virginiana
Dolichotis patagonum NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5.556 0.138 5.291 5.832 NA NA NA NA NA NA NA NA 7.289 0.940 5.663 9.285 NA NA NA NA 0 0 0 0 0 4227 5 0 124 20 Dolichotis patagonum Rodentia NA Dolichotis_patagonum
Eidolon helvum 17.843 0.544 16.821 18.934 NA NA NA NA NA NA NA NA 19.944 1.430 17.326 22.966 NA NA NA NA 14.742 0.444 13.893 15.627 NA NA NA NA NA NA NA NA 17.839 1.000 15.918 19.965 NA NA NA NA 648 2 0 96 3 620 0 0 164 15 Eidolon helvum Chiroptera NA Eidolon_helvum
Equus_africanus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 21.846 0.671 20.570 23.213 NA NA NA NA NA NA NA NA 24.877 1.041 22.924 26.997 NA NA NA NA 0 0 0 0 0 2097 1 2 346 24 Equus africanus Perissodactyla Replaced with wild ancestor Equus_africanus
Equus caballus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 18.693 0.387 17.990 19.497 NA NA NA NA NA NA NA NA 23.935 0.948 22.310 26.126 23.665 2.453 19.305 28.927 0 0 0 0 0 4254 1 8 1107 155 Equus caballus Perissodactyla NA Equus_caballus
Equus hemionus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 11.216 0.855 9.758 13.161 NA NA NA NA NA NA NA NA 30.044 13.545 15.316 63.573 NA NA NA NA 0 0 0 0 0 552 0 4 32 5 Equus hemionus Perissodactyla NA Equus_hemionus
Equus quagga NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14.141 0.395 13.398 14.927 NA NA NA NA NA NA NA NA 21.304 1.838 18.060 25.155 NA NA NA NA 0 0 0 0 0 3752 5 11 164 29 Equus quagga Perissodactyla NA Equus_quagga
Erythrocebus patas 14.035 0.476 13.119 14.979 14.689 1.810 11.462 18.541 NA NA NA NA NA NA NA NA NA NA NA NA 11.090 0.561 10.032 12.254 NA NA NA NA NA NA NA NA 11.528 1.614 8.767 15.160 NA NA NA NA 851 45 0 8 20 677 3 0 45 4 Erythrocebus patas Primates NA Erythrocebus_patas
Eudorcas thomsonii NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4.805 0.207 4.418 5.227 NA NA NA NA NA NA NA NA 10.071 1.399 7.757 13.322 NA NA NA NA 0 0 0 0 0 1573 0 0 86 6 Eudorcas thomsonii Artiodactyla NA Eudorcas_thomsonii
Eulemur coronatus 14.345 0.939 12.494 16.196 19.971 1.777 16.257 23.292 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 117 38 0 0 1 0 0 0 0 0 Eulemur coronatus Primates NA Eulemur_coronatus
Eulemur macaco 13.210 0.623 12.001 14.469 22.011 4.462 14.806 32.284 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 345 36 0 10 13 0 0 0 0 0 Eulemur macaco Primates NA Eulemur_macaco
Eulemur rubriventer 19.730 3.022 15.867 27.911 20.429 5.414 12.818 32.686 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 125 31 0 1 6 0 0 0 0 0 Eulemur rubriventer Primates NA Eulemur_rubriventer
Felis catus 12.777 0.330 12.129 13.431 NA NA NA NA NA NA NA NA 16.024 0.868 14.400 17.783 NA NA NA NA 9.530 0.445 8.657 10.408 NA NA NA NA NA NA NA NA 13.379 0.956 11.551 15.337 14.863 2.042 11.076 19.168 1054 0 1 126 27 836 0 1 125 38 Felis catus Carnivora NA Felis_catus
Giraffa camelopardalis 13.447 0.218 13.030 13.879 16.394 1.290 14.025 19.033 15.366 1.423 12.772 18.329 NA NA NA NA 16.270 1.206 14.032 18.741 10.234 0.209 9.838 10.657 NA NA NA NA 13.573 3.216 8.476 21.036 12.749 0.990 10.922 14.756 NA NA NA NA 3225 141 105 0 54 3368 23 31 160 10 Giraffa camelopardalis Artiodactyla NA Giraffa_camelopardalis
Gorilla gorilla 27.254 1.760 24.251 31.194 39.009 5.003 31.489 50.459 NA NA NA NA NA NA NA NA 34.652 3.795 28.622 43.739 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 350 188 0 3 86 0 0 0 0 0 Gorilla gorilla Primates NA Gorilla_gorilla
Hemitragus jemlahicus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.485 0.384 6.800 8.314 NA NA NA NA NA NA NA NA 9.667 1.369 7.347 12.640 NA NA NA NA 0 0 0 0 0 1109 0 0 46 7 Hemitragus jemlahicus Artiodactyla NA Hemitragus_jemlahicus
Hippopotamus amphibius 33.946 2.289 30.540 39.168 55.360 16.293 32.666 94.446 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 651 33 1 0 6 0 0 0 0 0 Hippopotamus amphibius Artiodactyla NA Hippopotamus_amphibius
Hippotragus niger NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8.087 0.381 7.375 8.870 NA NA NA NA NA NA NA NA 8.263 1.650 5.593 12.048 NA NA NA NA 0 0 0 0 0 2053 1 5 30 8 Hippotragus niger Artiodactyla NA Hippotragus_niger
Hydrochoerus hydrochaeris 5.898 0.131 5.650 6.159 5.987 1.090 4.189 8.415 NA NA NA NA NA NA NA NA NA NA NA NA 5.689 0.153 5.407 6.008 NA NA NA NA NA NA NA NA 5.412 0.483 4.542 6.407 NA NA NA NA 3831 33 0 4 7 3456 13 0 134 25 Hydrochoerus hydrochaeris Rodentia NA Hydrochoerus_hydrochaeris
Hylobates lar 20.808 1.388 18.532 24.157 23.560 4.606 16.285 33.890 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 718 58 2 15 13 0 0 0 0 0 Hylobates lar Primates NA Hylobates_lar
Hystrix indica NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 15.787 0.608 14.632 17.009 NA NA NA NA NA NA NA NA 17.767 3.190 12.464 24.763 NA NA NA NA 0 0 0 0 0 863 3 0 39 9 Hystrix indica Rodentia NA Hystrix_indica
Kobus ellipsiprymnus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9.121 0.355 8.446 9.828 NA NA NA NA NA NA NA NA 13.388 1.007 11.594 15.549 NA NA NA NA 0 0 0 0 0 2202 0 2 141 5 Kobus ellipsiprymnus Artiodactyla NA Kobus_ellipsiprymnus
Kobus leche NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.893 0.374 7.186 8.649 NA NA NA NA NA NA NA NA 11.145 2.104 7.814 15.963 NA NA NA NA 0 0 0 0 0 2201 0 0 82 29 Kobus leche Artiodactyla NA Kobus_leche
Kobus megaceros NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.186 0.269 6.674 7.734 NA NA NA NA NA NA NA NA 8.108 0.915 6.499 10.010 NA NA NA NA 0 0 0 0 0 1139 6 0 65 12 Kobus megaceros Artiodactyla NA Kobus_megaceros
Lama glama NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14.548 0.364 13.856 15.285 NA NA NA NA NA NA NA NA 13.513 0.803 12.067 15.164 15.180 1.856 11.871 19.121 0 0 0 0 0 4493 0 0 217 35 Lama glama Artiodactyla NA Lama_glama
Lama guanicoe NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 11.551 0.421 10.740 12.412 NA NA NA NA NA NA NA NA 13.760 1.577 10.834 17.001 NA NA NA NA 0 0 0 0 0 1484 0 0 71 12 Lama guanicoe Artiodactyla NA Lama_guanicoe
Lemur catta 15.105 0.236 14.651 15.570 18.251 1.082 16.231 20.460 NA NA NA NA 14.695 1.689 11.646 18.232 15.234 1.369 12.683 18.114 16.797 0.307 16.221 17.428 14.635 3.782 8.697 23.141 NA NA NA NA 17.989 1.110 15.967 20.211 16.153 2.891 11.373 22.501 5335 383 1 48 79 6379 46 0 404 30 Lemur catta Primates NA Lemur_catta
Leontopithecus chrysomelas 7.880 0.294 7.327 8.473 10.992 1.176 8.818 13.503 NA NA NA NA NA NA NA NA 8.609 1.019 6.726 10.722 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 703 73 0 16 41 0 0 0 0 0 Leontopithecus chrysomelas Primates NA Leontopithecus_chrysomelas
Leontopithecus rosalia 9.222 0.301 8.642 9.814 10.705 0.916 9.038 12.580 NA NA NA NA NA NA NA NA 8.939 0.780 7.520 10.531 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 914 130 0 17 77 0 0 0 0 0 Leontopithecus rosalia Primates NA Leontopithecus_rosalia
Leptailurus serval 12.627 0.428 11.810 13.490 NA NA NA NA NA NA NA NA 13.472 1.880 10.153 17.418 NA NA NA NA 12.112 0.381 11.389 12.884 NA NA NA NA NA NA NA NA 14.048 1.279 11.734 16.688 NA NA NA NA 1399 25 0 44 15 1441 5 0 71 6 Leptailurus serval Carnivora NA Leptailurus_serval
Lycaon pictus 7.120 0.190 6.757 7.503 5.741 0.588 4.699 7.029 NA NA NA NA 5.742 0.477 4.882 6.721 6.044 0.475 5.184 7.031 8.051 0.173 7.723 8.391 8.700 0.682 7.435 10.112 NA NA NA NA 6.247 0.841 4.809 8.130 7.319 0.604 6.222 8.596 1474 84 1 94 82 1774 73 0 46 54 Lycaon pictus Carnivora NA Lycaon_pictus
Lynx lynx 13.562 0.325 12.920 14.203 15.797 2.547 11.404 21.417 NA NA NA NA NA NA NA NA NA NA NA NA 14.063 0.314 13.456 14.692 NA NA NA NA NA NA NA NA 12.272 0.907 10.601 14.098 NA NA NA NA 1415 38 1 12 16 1349 17 1 61 14 Lynx lynx Carnivora NA Lynx_lynx
Lynx rufus 15.828 0.375 15.095 16.551 NA NA NA NA NA NA NA NA 17.111 1.003 15.211 19.139 NA NA NA NA 14.094 0.367 13.361 14.789 NA NA NA NA NA NA NA NA 16.781 0.788 15.302 18.378 NA NA NA NA 828 3 0 54 6 784 1 0 94 10 Lynx rufus Carnivora NA Lynx_rufus
Macaca fascicularis 21.541 0.764 20.187 23.156 19.348 2.713 14.443 25.174 NA NA NA NA 22.473 2.429 18.107 27.753 NA NA NA NA 13.483 0.804 12.090 15.205 NA NA NA NA NA NA NA NA 15.360 3.057 10.513 22.871 NA NA NA NA 1408 72 0 88 7 1008 2 0 93 4 Macaca fascicularis Primates NA Macaca_fascicularis
Macaca fuscata 16.997 0.431 16.158 17.858 18.794 1.379 16.244 21.765 NA NA NA NA 28.311 3.557 22.001 36.005 17.734 1.573 14.855 20.909 13.806 0.499 12.871 14.833 NA NA NA NA NA NA NA NA 17.758 1.585 14.925 21.226 17.462 3.038 12.257 24.041 1325 125 7 76 57 1315 6 0 142 31 Macaca fuscata Primates NA Macaca_fuscata
Macaca leonina NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14.811 2.890 10.226 21.177 NA NA NA NA NA NA NA NA 13.286 3.525 8.021 21.475 NA NA NA NA 0 0 0 0 0 66 0 0 41 0 Macaca leonina Primates NA Macaca_leonina
Macaca mulatta 18.107 0.530 17.064 19.155 NA NA NA NA NA NA NA NA 25.874 3.948 18.423 33.710 NA NA NA NA 14.241 0.703 12.955 15.663 NA NA NA NA NA NA NA NA 21.630 1.971 18.032 25.703 NA NA NA NA 1054 17 0 52 4 766 1 0 110 8 Macaca mulatta Primates NA Macaca_mulatta
Macaca nemestrina NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 16.973 1.184 14.959 19.505 NA NA NA NA NA NA NA NA 21.832 4.177 15.015 31.234 NA NA NA NA 0 0 0 0 0 404 3 0 30 7 Macaca nemestrina Primates NA Macaca_nemestrina
Macaca nigra 12.546 0.601 11.403 13.785 11.786 1.400 9.213 14.711 NA NA NA NA NA NA NA NA NA NA NA NA 11.770 0.686 10.501 13.183 NA NA NA NA NA NA NA NA 7.753 0.988 6.046 9.912 NA NA NA NA 429 55 1 6 24 482 18 0 68 1 Macaca nigra Primates NA Macaca_nigra
Macaca silenus 17.665 0.640 16.484 18.975 18.782 2.549 14.169 24.276 NA NA NA NA NA NA NA NA NA NA NA NA 14.731 0.596 13.605 15.937 NA NA NA NA NA NA NA NA 15.467 1.615 12.510 18.855 NA NA NA NA 578 62 0 19 21 564 28 0 50 11 Macaca silenus Primates NA Macaca_silenus
Macaca sylvanus 13.233 0.519 12.253 14.307 16.434 1.284 14.172 19.073 NA NA NA NA NA NA NA NA NA NA NA NA 11.545 0.624 10.430 12.896 NA NA NA NA NA NA NA NA 15.948 1.528 13.353 19.392 NA NA NA NA 855 213 0 17 24 781 20 1 240 10 Macaca sylvanus Primates NA Macaca_sylvanus
Macaca tonkeana 15.379 1.437 12.716 18.300 9.950 2.043 6.303 14.325 NA NA NA NA NA NA NA NA NA NA NA NA 12.811 1.110 10.748 15.042 NA NA NA NA NA NA NA NA 13.365 2.137 9.368 17.763 NA NA NA NA 93 37 0 5 0 88 0 0 33 1 Macaca tonkeana Primates NA Macaca_tonkeana
Macropus eugenii NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4.603 0.201 4.230 5.002 NA NA NA NA NA NA NA NA 6.889 1.307 4.781 9.847 NA NA NA NA 0 0 0 0 0 1007 0 0 36 1 Macropus eugenii Diprotodontia NA Macropus_eugenii
Macropus fuliginosus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.123 0.382 6.428 7.917 NA NA NA NA NA NA NA NA 8.455 1.111 6.575 10.921 NA NA NA NA 0 0 0 0 0 887 0 0 79 10 Macropus fuliginosus Diprotodontia NA Macropus_fuliginosus
Macropus giganteus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4.026 0.196 3.652 4.420 NA NA NA NA NA NA NA NA 9.139 1.063 7.320 11.534 NA NA NA NA 0 0 0 0 0 1993 0 0 147 5 Macropus giganteus Diprotodontia NA Macropus_giganteus
Macropus parma NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4.954 0.186 4.614 5.359 NA NA NA NA NA NA NA NA 6.590 1.202 4.696 9.382 NA NA NA NA 0 0 0 0 0 1442 0 0 40 17 Macropus parma Diprotodontia NA Macropus_parma
Macropus robustus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 6.372 0.360 5.717 7.110 NA NA NA NA NA NA NA NA 6.719 1.042 4.973 9.007 NA NA NA NA 0 0 0 0 0 560 0 0 33 16 Macropus robustus Diprotodontia NA Macropus_robustus
Macropus rufogriseus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5.746 0.116 5.530 5.981 NA NA NA NA NA NA NA NA 7.032 0.401 6.308 7.849 4.348 0.613 3.305 5.696 0 0 0 0 0 6934 0 0 586 65 Macropus rufogriseus Diprotodontia NA Macropus_rufogriseus
Macropus rufus 7.007 0.106 6.798 7.212 6.714 0.931 5.122 8.779 NA NA NA NA NA NA NA NA NA NA NA NA 5.423 0.123 5.186 5.663 NA NA NA NA NA NA NA NA 6.666 0.382 5.941 7.454 NA NA NA NA 4520 39 0 4 21 3879 2 1 242 27 Macropus rufus Diprotodontia NA Macropus_rufus
Mephitis mephitis 5.656 0.150 5.366 5.960 NA NA NA NA NA NA NA NA 7.512 0.719 6.219 8.993 NA NA NA NA 5.538 0.191 5.176 5.928 NA NA NA NA NA NA NA NA 5.810 0.443 5.007 6.736 NA NA NA NA 1015 7 0 41 5 996 4 0 128 12 Mephitis mephitis Carnivora NA Mephitis_mephitis
Mungos mungo NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9.289 0.283 8.747 9.871 NA NA NA NA NA NA NA NA 9.315 1.649 6.546 12.958 NA NA NA NA 0 0 0 0 0 1415 9 0 46 19 Mungos mungo Carnivora NA Mungos_mungo
Muntiacus reevesi 8.722 0.193 8.351 9.115 9.490 1.385 7.110 12.580 NA NA NA NA NA NA NA NA NA NA NA NA 7.989 0.236 7.543 8.456 NA NA NA NA NA NA NA NA 12.857 1.431 10.278 15.940 NA NA NA NA 2343 33 1 11 11 2288 13 0 83 24 Muntiacus reevesi Artiodactyla NA Muntiacus_reevesi
Mustela nigripes 5.146 0.100 4.953 5.347 NA NA NA NA NA NA NA NA 5.104 0.258 4.607 5.616 NA NA NA NA 4.512 0.087 4.344 4.686 NA NA NA NA NA NA NA NA 4.314 0.201 3.934 4.716 NA NA NA NA 2502 0 0 56 10 2560 0 0 79 9 Mustela nigripes Carnivora NA Mustela_nigripes
Mustela putorius 5.355 0.116 5.130 5.590 3.989 0.645 2.910 5.442 NA NA NA NA 6.268 0.333 5.647 6.975 6.585 0.825 5.092 8.317 5.050 0.109 4.836 5.267 NA NA NA NA NA NA NA NA 4.755 0.209 4.357 5.188 4.585 0.635 3.462 5.952 1824 35 0 229 38 2014 11 0 383 36 Mustela putorius Carnivora NA Mustela_putorius
Myocastor coypus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 2.672 0.151 2.391 2.984 NA NA NA NA NA NA NA NA 2.990 0.612 2.001 4.395 NA NA NA NA 0 0 0 0 0 710 0 0 41 2 Myocastor coypus Rodentia NA Myocastor_coypus
Nasua narica NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9.835 0.523 8.857 10.914 NA NA NA NA NA NA NA NA 9.667 0.966 7.947 11.750 NA NA NA NA 0 0 0 0 0 378 0 0 57 17 Nasua narica Carnivora NA Nasua_narica
Nasua nasua 9.598 0.187 9.242 9.968 9.685 1.356 7.315 12.713 NA NA NA NA 10.327 1.570 7.703 13.817 8.077 0.916 6.457 10.040 8.803 0.258 8.301 9.314 NA NA NA NA NA NA NA NA 10.020 0.719 8.699 11.490 8.762 1.479 6.356 12.016 2776 37 0 40 35 2229 12 0 239 35 Nasua nasua Carnivora NA Nasua_nasua
Nyctereutes procyonoides NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9.144 0.401 8.393 9.971 NA NA NA NA NA NA NA NA 7.867 1.396 5.514 10.977 NA NA NA NA 0 0 0 0 0 519 1 4 35 2 Nyctereutes procyonoides Carnivora NA Nyctereutes_procyonoides
Octodon degus 4.347 0.197 3.982 4.746 5.858 0.947 4.289 7.991 NA NA NA NA NA NA NA NA NA NA NA NA 3.619 0.174 3.289 3.979 NA NA NA NA NA NA NA NA 3.408 0.328 2.815 4.099 NA NA NA NA 807 85 0 2 0 670 0 0 187 6 Octodon degus Rodentia NA Octodon_degus
Odocoileus virginianus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8.171 0.288 7.631 8.769 NA NA NA NA NA NA NA NA 10.430 0.954 8.697 12.423 NA NA NA NA 0 0 0 0 0 2429 0 0 115 5 Odocoileus virginianus Artiodactyla NA Odocoileus_virginianus
Oryctolagus cuniculus 4.762 0.090 4.590 4.941 NA NA NA NA NA NA NA NA 6.515 0.379 5.824 7.310 6.276 0.990 4.627 8.559 5.467 0.129 5.222 5.724 NA NA NA NA NA NA NA NA 6.095 0.267 5.602 6.642 4.991 0.690 3.786 6.557 4061 1 0 481 37 2762 3 0 831 58 Oryctolagus cuniculus Lagomorpha NA Oryctolagus_cuniculus
Oryx dammah NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8.691 0.187 8.342 9.074 NA NA NA NA NA NA NA NA 12.441 0.843 10.904 14.211 NA NA NA NA 0 0 0 0 0 3999 6 4 168 21 Oryx dammah Artiodactyla NA Oryx_dammah
Oryx gazella NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8.477 0.329 7.861 9.155 NA NA NA NA NA NA NA NA 11.907 1.323 9.440 14.574 NA NA NA NA 0 0 0 0 0 1517 0 1 34 3 Oryx gazella Artiodactyla NA Oryx_gazella
Ovis aries NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8.003 0.179 7.656 8.369 NA NA NA NA NA NA NA NA 10.997 0.638 9.824 12.302 15.025 1.958 11.709 19.278 0 0 0 0 0 13677 1 8 708 129 Ovis aries Artiodactyla NA Ovis_aries
Ovis canadensis NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 6.304 0.269 5.791 6.857 NA NA NA NA NA NA NA NA 9.764 1.184 7.673 12.293 NA NA NA NA 0 0 0 0 0 873 0 0 32 0 Ovis canadensis Artiodactyla NA Ovis_canadensis
Pan paniscus 49.931 22.105 27.009 109.421 33.258 16.367 15.238 77.027 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 121 30 0 0 13 0 0 0 0 0 Pan paniscus Primates NA Pan_paniscus
Pan troglodytes 31.762 0.952 29.940 33.658 37.235 2.330 32.882 42.162 NA NA NA NA NA NA NA NA 31.094 2.182 26.994 35.690 26.292 1.006 24.525 28.503 NA NA NA NA NA NA NA NA 41.443 3.754 35.195 49.842 23.236 3.827 16.516 31.633 1485 344 0 28 151 1485 8 0 245 30 Pan troglodytes Primates NA Pan_troglodytes
Panthera leo 13.143 0.196 12.763 13.526 15.558 0.739 14.171 17.089 NA NA NA NA 13.376 0.706 12.054 14.827 12.356 0.509 11.398 13.417 14.244 0.226 13.805 14.676 NA NA NA NA NA NA NA NA 12.477 0.653 11.244 13.836 11.703 1.212 9.530 14.315 4402 393 11 202 206 4598 16 0 223 35 Panthera leo Carnivora NA Panthera_leo
Panthera onca 15.371 0.351 14.697 16.086 15.675 1.552 12.815 18.978 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 865 34 0 22 15 0 0 0 0 0 Panthera onca Carnivora NA Panthera_onca
Panthera pardus 14.678 0.316 14.069 15.315 15.016 2.041 11.468 19.345 NA NA NA NA 13.521 1.473 10.908 16.648 11.294 1.177 9.160 13.789 15.414 0.333 14.766 16.063 NA NA NA NA NA NA NA NA 12.067 1.636 9.291 15.589 NA NA NA NA 1890 39 1 36 34 1977 8 0 31 8 Panthera pardus Carnivora NA Panthera_pardus
Panthera tigris 12.506 0.155 12.200 12.814 12.280 0.782 10.847 13.894 NA NA NA NA 12.220 0.720 10.876 13.703 10.609 0.607 9.507 11.862 12.571 0.171 12.243 12.919 NA NA NA NA NA NA NA NA 10.928 0.616 9.761 12.166 10.555 0.885 8.926 12.436 4387 139 3 96 98 4175 26 1 126 49 Panthera tigris Carnivora NA Panthera_tigris
Papio anubis NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 14.340 1.348 12.032 17.357 NA NA NA NA NA NA NA NA 31.038 9.316 19.791 55.759 NA NA NA NA 0 0 0 0 0 248 0 0 53 0 Papio anubis Primates NA Papio_anubis
Papio hamadryas 14.973 0.316 14.362 15.570 19.734 0.876 18.055 21.501 NA NA NA NA 19.323 1.012 17.439 21.421 17.694 1.138 15.583 19.943 12.208 0.320 11.600 12.848 NA NA NA NA NA NA NA NA 17.556 0.985 15.720 19.611 15.905 1.631 12.998 19.379 2204 297 0 172 87 2324 7 0 244 70 Papio hamadryas Primates NA Papio_hamadryas
Papio papio 15.794 0.737 14.443 17.308 15.589 2.025 11.946 19.911 NA NA NA NA NA NA NA NA NA NA NA NA 12.385 0.637 11.195 13.677 NA NA NA NA NA NA NA NA 11.245 1.884 7.897 15.364 NA NA NA NA 445 39 0 20 5 479 21 0 39 1 Papio papio Primates NA Papio_papio
Pecari tajacu NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 10.055 0.351 9.387 10.759 NA NA NA NA NA NA NA NA 17.439 1.584 14.515 20.759 NA NA NA NA 0 0 0 0 0 1601 0 0 94 8 Pecari tajacu Artiodactyla NA Pecari_tajacu
Petaurus breviceps NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 7.824 0.227 7.400 8.271 NA NA NA NA NA NA NA NA 6.819 0.661 5.614 8.231 NA NA NA NA 0 0 0 0 0 1582 0 0 108 2 Petaurus breviceps Diprotodontia NA Petaurus_breviceps
Petrogale xanthopus 5.919 0.198 5.531 6.323 6.269 0.866 4.735 8.103 NA NA NA NA NA NA NA NA NA NA NA NA 4.168 0.174 3.828 4.506 NA NA NA NA NA NA NA NA 6.391 0.660 5.196 7.779 NA NA NA NA 984 37 5 0 2 1022 6 0 42 1 Petrogale xanthopus Diprotodontia NA Petrogale_xanthopus
Phacochoerus africanus 9.417 0.324 8.801 10.061 10.110 1.186 8.012 12.587 NA NA NA NA NA NA NA NA NA NA NA NA 8.567 0.314 7.964 9.197 NA NA NA NA NA NA NA NA 8.612 1.256 6.393 11.275 NA NA NA NA 630 42 13 8 8 687 6 1 31 5 Phacochoerus africanus Artiodactyla NA Phacochoerus_africanus
Phascolarctos cinereus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4.855 0.139 4.586 5.131 NA NA NA NA NA NA NA NA 10.923 1.722 7.993 14.602 NA NA NA NA 0 0 0 0 0 2317 0 0 38 29 Phascolarctos cinereus Diprotodontia NA Phascolarctos_cinereus
Pithecia pithecia 10.014 0.587 8.948 11.226 15.809 2.416 11.722 21.049 NA NA NA NA NA NA NA NA 14.867 2.226 11.175 19.699 13.566 0.769 12.289 15.247 NA NA NA NA NA NA NA NA 16.487 3.240 11.210 23.796 NA NA NA NA 578 76 0 5 38 750 17 0 50 0 Pithecia pithecia Primates NA Pithecia_pithecia
Pongo abelii 27.943 2.351 24.359 33.223 36.273 6.061 26.781 50.706 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 370 59 0 5 16 0 0 0 0 0 Pongo abelii Primates NA Pongo_abelii
Pongo pygmaeus 28.589 2.221 24.937 33.521 40.132 6.274 30.903 56.056 NA NA NA NA NA NA NA NA 37.512 6.347 27.935 51.644 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 472 113 0 6 31 0 0 0 0 0 Pongo pygmaeus Primates NA Pongo_pygmaeus
Potamochoerus porcus 9.338 0.309 8.742 9.960 9.090 0.969 7.301 11.113 NA NA NA NA NA NA NA NA NA NA NA NA 9.516 0.331 8.880 10.195 NA NA NA NA NA NA NA NA 10.647 1.242 8.448 13.323 NA NA NA NA 824 45 1 3 7 759 9 9 48 2 Potamochoerus porcus Artiodactyla NA Potamochoerus_porcus
Potos flavus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 21.562 1.091 19.484 23.715 NA NA NA NA NA NA NA NA 28.796 4.010 21.549 37.007 NA NA NA NA 0 0 0 0 0 458 1 0 31 2 Potos flavus Carnivora NA Potos_flavus
Procavia capensis NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4.073 0.130 3.825 4.335 5.512 0.838 4.103 7.364 NA NA NA NA 4.324 0.614 3.239 5.660 NA NA NA NA 0 0 0 0 0 1457 74 1 43 2 Procavia capensis Hyracoidea NA Procavia_capensis
Procyon lotor 10.743 0.241 10.270 11.233 NA NA NA NA NA NA NA NA 11.994 0.918 10.318 13.850 NA NA NA NA 9.226 0.253 8.737 9.738 NA NA NA NA NA NA NA NA 11.788 0.679 10.546 13.199 8.898 1.079 6.986 11.169 2351 14 0 289 25 2259 9 1 478 52 Procyon lotor Carnivora NA Procyon_lotor
Propithecus coquereli 6.344 1.193 4.221 8.893 13.351 1.364 10.642 15.949 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 42 41 0 0 0 0 0 0 0 0 Propithecus coquereli Primates NA Propithecus_coquereli
Pteropus rodricensis 11.343 0.332 10.714 11.986 13.500 1.646 10.614 16.994 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1226 113 0 26 14 0 0 0 0 0 Pteropus rodricensis Chiroptera NA Pteropus_rodricensis
Puma concolor 12.676 0.248 12.180 13.150 NA NA NA NA NA NA NA NA 14.844 0.864 13.225 16.640 NA NA NA NA 11.564 0.240 11.087 12.048 NA NA NA NA NA NA NA NA 13.678 0.684 12.363 15.044 NA NA NA NA 1265 11 0 82 28 1163 0 0 94 17 Puma concolor Carnivora NA Puma_concolor
Rangifer tarandus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 5.755 0.171 5.427 6.095 NA NA NA NA NA NA NA NA 8.113 0.978 6.366 10.192 NA NA NA NA 0 0 0 0 0 3302 9 0 87 15 Rangifer tarandus Artiodactyla NA Rangifer_tarandus
Rattus norvegicus 1.899 0.039 1.823 1.978 NA NA NA NA NA NA NA NA 2.015 0.173 1.699 2.375 NA NA NA NA 1.798 0.043 1.715 1.882 NA NA NA NA NA NA NA NA 1.757 0.117 1.546 1.998 NA NA NA NA 2473 5 0 134 0 1435 0 0 158 2 Rattus norvegicus Rodentia NA Rattus_norvegicus
Rousettus aegyptiacus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9.055 0.227 8.614 9.498 NA NA NA NA NA NA NA NA 5.897 0.371 5.208 6.652 NA NA NA NA 0 0 0 0 0 1474 0 0 165 1 Rousettus aegyptiacus Chiroptera NA Rousettus_aegyptiacus
Saguinus bicolor 7.996 0.686 6.779 9.486 13.691 2.551 9.929 20.180 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 206 54 0 6 10 0 0 0 0 0 Saguinus bicolor Primates NA Saguinus_bicolor
Saguinus imperator 7.119 0.208 6.736 7.534 8.708 0.881 7.112 10.490 NA NA NA NA NA NA NA NA NA NA NA NA 8.251 0.231 7.810 8.712 8.402 1.627 5.647 11.988 NA NA NA NA NA NA NA NA NA NA NA NA 1023 76 2 14 17 1222 30 0 4 7 Saguinus imperator Primates NA Saguinus_imperator
Saguinus oedipus 9.482 0.219 9.072 9.934 12.162 1.082 10.180 14.455 NA NA NA NA NA NA NA NA 10.336 0.893 8.720 12.196 10.488 0.203 10.106 10.899 12.775 3.093 8.003 20.142 NA NA NA NA 11.744 1.282 9.432 14.434 NA NA NA NA 2958 172 1 27 94 3490 30 0 97 16 Saguinus oedipus Primates NA Saguinus_oedipus
Saimiri boliviensis 12.651 0.287 12.110 13.231 10.180 1.997 6.784 14.532 NA NA NA NA NA NA NA NA 11.848 1.521 9.152 15.123 12.063 0.495 11.201 13.166 NA NA NA NA NA NA NA NA 10.125 1.381 7.803 13.158 13.755 2.124 10.171 18.405 1801 40 0 17 34 1598 16 0 115 49 Saimiri boliviensis Primates NA Saimiri_boliviensis
Saimiri sciureus 11.381 0.224 10.941 11.830 16.822 2.669 12.212 22.609 NA NA NA NA 13.440 2.604 9.028 19.294 NA NA NA NA 9.900 0.302 9.333 10.519 NA NA NA NA NA NA NA NA 13.987 1.898 10.617 17.999 NA NA NA NA 3541 60 3 31 6 3099 0 0 119 0 Saimiri sciureus Primates NA Saimiri_sciureus
Sapajus apella 23.058 0.677 21.802 24.455 45.491 11.272 28.102 72.275 NA NA NA NA NA NA NA NA NA NA NA NA 21.628 0.577 20.525 22.757 NA NA NA NA NA NA NA NA 20.700 2.044 16.881 24.976 NA NA NA NA 1524 39 0 26 15 1781 12 0 103 11 Sapajus apella Primates NA Sapajus_apella
Sapajus xanthosternos 20.891 5.576 13.979 35.582 36.640 18.919 19.960 86.062 NA NA NA NA NA NA NA NA NA NA NA NA 17.488 2.833 13.522 24.751 NA NA NA NA NA NA NA NA 27.673 11.442 15.534 59.134 NA NA NA NA 80 52 0 2 3 173 10 0 47 0 Sapajus xanthosternos Primates NA Sapajus_xanthosternos
Suricata suricatta 8.102 0.105 7.905 8.309 9.203 0.578 8.131 10.412 NA NA NA NA 7.248 0.696 6.025 8.747 7.237 0.715 5.957 8.763 8.552 0.091 8.373 8.732 8.350 1.279 6.191 11.164 NA NA NA NA 8.660 0.392 7.935 9.448 7.492 0.642 6.332 8.822 5887 209 1 76 51 6746 45 2 261 58 Suricata suricatta Carnivora NA Suricata_suricatta
Sus scrofa 9.311 0.158 9.009 9.630 NA NA NA NA NA NA NA NA 10.825 1.183 8.782 13.328 NA NA NA NA 9.180 0.242 8.721 9.679 NA NA NA NA NA NA NA NA 10.928 0.639 9.713 12.242 9.455 1.107 7.506 11.828 7430 23 0 64 2 5590 8 15 704 107 Sus scrofa Artiodactyla NA Sus_scrofa
Symphalangus syndactylus 18.701 1.554 16.117 22.211 33.362 8.041 23.562 54.174 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 364 74 0 6 24 0 0 0 0 0 Symphalangus syndactylus Primates NA Symphalangus_syndactylus
Tapirus terrestris 15.386 0.625 14.233 16.715 17.549 3.118 12.332 24.342 NA NA NA NA NA NA NA NA NA NA NA NA 15.093 0.626 13.926 16.390 NA NA NA NA NA NA NA NA 18.339 4.662 10.973 29.171 NA NA NA NA 724 47 7 1 9 817 14 17 52 2 Tapirus terrestris Perissodactyla NA Tapirus_terrestris
Theropithecus gelada 17.965 0.678 16.685 19.324 21.045 6.017 11.667 35.501 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 344 38 0 4 1 0 0 0 0 0 Theropithecus gelada Primates NA Theropithecus_gelada
Trachypithecus auratus 10.928 0.496 9.969 11.915 8.468 1.701 5.584 12.211 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 441 31 0 6 17 0 0 0 0 0 Trachypithecus auratus Primates NA Trachypithecus_auratus
Trachypithecus cristatus 10.830 1.120 8.951 13.396 18.269 6.934 9.806 35.536 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 187 31 0 6 4 0 0 0 0 0 Trachypithecus cristatus Primates NA Trachypithecus_cristatus
Trachypithecus francoisi 10.958 0.980 9.126 12.975 10.905 1.937 7.573 15.032 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 145 40 0 3 22 0 0 0 0 0 Trachypithecus francoisi Primates NA Trachypithecus_francoisi
Tragelaphus angasii NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 4.601 0.161 4.303 4.925 NA NA NA NA NA NA NA NA 5.136 1.015 3.463 7.451 NA NA NA NA 0 0 0 0 0 2219 4 4 32 0 Tragelaphus angasii Artiodactyla NA Tragelaphus_angasii
Tragelaphus oryx NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 8.789 0.177 8.448 9.149 NA NA NA NA NA NA NA NA 10.135 0.641 8.943 11.442 NA NA NA NA 0 0 0 0 0 4043 0 2 166 17 Tragelaphus oryx Artiodactyla NA Tragelaphus_oryx
Tragelaphus strepsiceros 8.294 0.175 7.965 8.650 6.667 0.885 5.138 8.563 NA NA NA NA NA NA NA NA NA NA NA NA 5.572 0.175 5.240 5.921 NA NA NA NA NA NA NA NA 5.393 0.696 4.160 6.917 NA NA NA NA 2217 34 8 2 15 1982 2 1 52 5 Tragelaphus strepsiceros Artiodactyla NA Tragelaphus_strepsiceros
Ursus americanus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 18.190 0.538 17.141 19.236 NA NA NA NA NA NA NA NA 19.729 1.285 17.348 22.392 NA NA NA NA 0 0 0 0 0 700 1 0 91 19 Ursus americanus Carnivora NA Ursus_americanus
Ursus arctos NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 21.217 0.634 20.023 22.514 NA NA NA NA NA NA NA NA 22.425 1.596 19.598 25.805 NA NA NA NA 0 0 0 0 0 1305 2 0 142 22 Ursus arctos Carnivora NA Ursus_arctos
Varecia rubra 17.014 0.507 16.037 18.010 19.606 1.504 16.897 22.865 NA NA NA NA NA NA NA NA 15.221 1.346 12.775 18.000 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 724 108 0 15 45 0 0 0 0 0 Varecia rubra Primates NA Varecia_rubra
Varecia variegata 15.690 0.401 14.925 16.493 17.280 1.854 13.941 21.082 NA NA NA NA NA NA NA NA 12.599 1.184 10.441 15.060 15.882 0.341 15.227 16.577 NA NA NA NA NA NA NA NA 17.830 1.768 14.634 21.516 NA NA NA NA 1419 91 0 24 59 1913 9 0 60 21 Varecia variegata Primates NA Varecia_variegata
Vicugna pacos NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 12.980 0.309 12.382 13.597 NA NA NA NA NA NA NA NA 13.888 0.825 12.368 15.608 13.248 1.455 10.585 16.257 0 0 0 0 0 2431 0 1 202 32 Vicugna pacos Artiodactyla NA Vicugna_pacos
Vicugna vicugna NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9.755 0.576 8.739 10.973 NA NA NA NA NA NA NA NA 11.968 2.762 7.560 18.244 NA NA NA NA 0 0 0 0 0 452 3 0 36 2 Vicugna vicugna Artiodactyla NA Vicugna_vicugna
Vulpes lagopus NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 6.938 0.260 6.435 7.462 NA NA NA NA NA NA NA NA 7.596 0.926 5.960 9.561 NA NA NA NA 0 0 0 0 0 721 9 0 38 9 Vulpes lagopus Carnivora NA Vulpes_lagopus
Vulpes vulpes 9.336 0.265 8.827 9.860 NA NA NA NA NA NA NA NA 11.004 1.775 7.939 14.794 NA NA NA NA 8.834 0.254 8.347 9.342 NA NA NA NA NA NA NA NA 10.314 1.024 8.410 12.411 NA NA NA NA 1180 5 0 35 12 1278 0 0 89 9 Vulpes vulpes Carnivora NA Vulpes_vulpes
Vulpes zerda NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 9.434 0.180 9.080 9.779 NA NA NA NA NA NA NA NA 8.395 0.736 7.028 9.962 NA NA NA NA 0 0 0 0 0 960 8 0 39 4 Vulpes zerda Carnivora NA Vulpes_zerda
Wallabia bicolor NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 3.957 0.193 3.601 4.367 NA NA NA NA NA NA NA NA 12.933 3.430 9.241 23.115 NA NA NA NA 0 0 0 0 0 941 4 0 80 12 Wallabia bicolor Diprotodontia NA Wallabia_bicolor
Zalophus californianus 16.660 0.339 15.998 17.312 17.690 3.301 11.806 24.530 NA NA NA NA NA NA NA NA NA NA NA NA 14.335 0.431 13.481 15.179 NA NA NA NA NA NA NA NA 15.569 1.204 13.298 18.029 NA NA NA NA 1316 35 3 2 11 1114 14 3 47 13 Zalophus californianus Carnivora NA Zalophus_californianus
Code
kable(dat_all, "html", escape = FALSE, digits = 3) %>% kable_styling("striped", position = "left", full_width = TRUE) %>% 
  scroll_box(width = "100%", 
    height = "500px")
species order phylogeny sex type yi vi obs_id sex_type
Aonyx cinerea Carnivora Aonyx_cinerea male hormonal 0.137 0.026 1 male_hormonal
Lemur catta Primates Lemur_catta male hormonal -0.138 0.067 2 male_hormonal
Lycaon pictus Carnivora Lycaon_pictus male hormonal 0.078 0.007 3 male_hormonal
Procavia capensis Hyracoidea Procavia_capensis male hormonal 0.303 0.024 4 male_hormonal
Saguinus imperator Primates Saguinus_imperator male hormonal 0.018 0.038 5 male_hormonal
Saguinus oedipus Primates Saguinus_oedipus male hormonal 0.197 0.059 6 male_hormonal
Suricata suricatta Carnivora Suricata_suricatta male hormonal -0.024 0.024 7 male_hormonal
Acinonyx jubatus Carnivora Acinonyx_jubatus male surgical 0.055 0.008 8 male_surgical
Addax nasomaculatus Artiodactyla Addax_nasomaculatus male surgical 0.169 0.008 9 male_surgical
Aepyceros melampus Artiodactyla Aepyceros_melampus male surgical 0.387 0.015 10 male_surgical
Alouatta caraya Primates Alouatta_caraya male surgical 0.040 0.024 11 male_surgical
Ammotragus lervia Artiodactyla Ammotragus_lervia male surgical 0.037 0.006 12 male_surgical
Antidorcas marsupialis Artiodactyla Antidorcas_marsupialis male surgical -0.097 0.027 13 male_surgical
Antilope cervicapra Artiodactyla Antilope_cervicapra male surgical 0.526 0.006 14 male_surgical
Aonyx cinerea Carnivora Aonyx_cinerea male surgical 0.033 0.006 15 male_surgical
Arctictis binturong Carnivora Arctictis_binturong male surgical 0.042 0.015 16 male_surgical
Artibeus jamaicensis Chiroptera Artibeus_jamaicensis male surgical 0.567 0.023 17 male_surgical
Ateles geoffroyi Primates Ateles_geoffroyi male surgical -0.051 0.015 18 male_surgical
Axis axis Artiodactyla Axis_axis male surgical -0.572 0.113 19 male_surgical
Bison bison Artiodactyla Bison_bison male surgical 0.046 0.007 20 male_surgical
Bos grunniens Artiodactyla Bos_grunniens male surgical 0.109 0.028 21 male_surgical
Bos javanicus Artiodactyla Bos_javanicus male surgical -0.202 0.040 22 male_surgical
Bos taurus Artiodactyla Bos_taurus male surgical 0.341 0.009 23 male_surgical
Boselaphus tragocamelus Artiodactyla Boselaphus_tragocamelus male surgical -0.070 0.030 24 male_surgical
Bubalus arnee Artiodactyla Bubalus_arnee male surgical 0.588 0.020 25 male_surgical
Callithrix jacchus Primates Callithrix_jacchus male surgical 0.367 0.017 26 male_surgical
Camelus bactrianus Artiodactyla Camelus_bactrianus male surgical -0.139 0.009 27 male_surgical
Camelus dromedarius Artiodactyla Camelus_dromedarius male surgical 0.025 0.013 28 male_surgical
Canis latrans Carnivora Canis_latrans male surgical 0.329 0.010 29 male_surgical
Canis lupus Carnivora Canis_lupus male surgical -0.021 0.002 30 male_surgical
Capra aegagrus Artiodactyla Capra_aegagrus male surgical 0.304 0.047 31 male_surgical
Capra falconeri Artiodactyla Capra_falconeri male surgical 0.070 0.024 32 male_surgical
Capra hircus Artiodactyla Capra_hircus male surgical 0.022 0.001 33 male_surgical
Capra nubiana Artiodactyla Capra_nubiana male surgical 0.201 0.016 34 male_surgical
Carollia perspicillata Chiroptera Carollia_perspicillata male surgical 0.981 0.045 35 male_surgical
Cavia porcellus Rodentia Cavia_porcellus male surgical 0.106 0.006 36 male_surgical
Cebus capucinus Primates Cebus_capucinus male surgical 0.864 0.309 37 male_surgical
Cervus canadensis Artiodactyla Cervus_canadensis male surgical 0.456 0.023 38 male_surgical
Cervus elaphus Artiodactyla Cervus_elaphus male surgical -0.108 0.014 39 male_surgical
Cervus nippon Artiodactyla Cervus_nippon male surgical -0.251 0.025 40 male_surgical
Chinchilla lanigera Rodentia Chinchilla_lanigera male surgical 0.112 0.023 41 male_surgical
Chlorocebus aethiops Primates Chlorocebus_aethiops male surgical 0.215 0.069 42 male_surgical
Colobus guereza Primates Colobus_guereza male surgical 0.017 0.016 43 male_surgical
Connochaetes taurinus Artiodactyla Connochaetes_taurinus male surgical 0.348 0.010 44 male_surgical
Cynomys ludovicianus Rodentia Cynomys_ludovicianus male surgical -0.071 0.010 45 male_surgical
Dama dama Artiodactyla Dama_dama male surgical 0.173 0.017 46 male_surgical
Damaliscus pygargus Artiodactyla Damaliscus_pygargus male surgical 0.078 0.026 47 male_surgical
Desmodus rotundus Chiroptera Desmodus_rotundus male surgical 0.517 0.015 48 male_surgical
Didelphis virginiana Didelphimorphia Didelphis_virginiana male surgical 0.440 0.015 49 male_surgical
Dolichotis patagonum Rodentia Dolichotis_patagonum male surgical 0.272 0.017 50 male_surgical
Eidolon helvum Chiroptera Eidolon_helvum male surgical 0.191 0.004 51 male_surgical
Equus_africanus Perissodactyla Equus_africanus male surgical 0.130 0.003 52 male_surgical
Equus caballus Perissodactyla Equus_caballus male surgical 0.247 0.002 53 male_surgical
Equus hemionus Perissodactyla Equus_hemionus male surgical 0.985 0.209 54 male_surgical
Equus quagga Perissodactyla Equus_quagga male surgical 0.410 0.008 55 male_surgical
Erythrocebus patas Primates Erythrocebus_patas male surgical 0.039 0.022 56 male_surgical
Eudorcas thomsonii Artiodactyla Eudorcas_thomsonii male surgical 0.740 0.021 57 male_surgical
Felis catus Carnivora Felis_catus male surgical 0.339 0.007 58 male_surgical
Giraffa camelopardalis Artiodactyla Giraffa_camelopardalis male surgical 0.220 0.006 59 male_surgical
Hemitragus jemlahicus Artiodactyla Hemitragus_jemlahicus male surgical 0.256 0.023 60 male_surgical
Hippotragus niger Artiodactyla Hippotragus_niger male surgical 0.022 0.042 61 male_surgical
Hydrochoerus hydrochaeris Rodentia Hydrochoerus_hydrochaeris male surgical -0.050 0.009 62 male_surgical
Hystrix indica Rodentia Hystrix_indica male surgical 0.118 0.034 63 male_surgical
Kobus ellipsiprymnus Artiodactyla Kobus_ellipsiprymnus male surgical 0.384 0.007 64 male_surgical
Kobus leche Artiodactyla Kobus_leche male surgical 0.345 0.038 65 male_surgical
Kobus megaceros Artiodactyla Kobus_megaceros male surgical 0.121 0.014 66 male_surgical
Lama glama Artiodactyla Lama_glama male surgical -0.074 0.004 67 male_surgical
Lama guanicoe Artiodactyla Lama_guanicoe male surgical 0.175 0.014 68 male_surgical
Lemur catta Primates Lemur_catta male surgical 0.069 0.004 69 male_surgical
Leptailurus serval Carnivora Leptailurus_serval male surgical 0.148 0.009 70 male_surgical
Lycaon pictus Carnivora Lycaon_pictus male surgical -0.254 0.019 71 male_surgical
Lynx lynx Carnivora Lynx_lynx male surgical -0.136 0.006 72 male_surgical
Lynx rufus Carnivora Lynx_rufus male surgical 0.174 0.003 73 male_surgical
Macaca fascicularis Primates Macaca_fascicularis male surgical 0.130 0.043 74 male_surgical
Macaca fuscata Primates Macaca_fuscata male surgical 0.252 0.009 75 male_surgical
Macaca leonina Primates Macaca_leonina male surgical -0.109 0.108 76 male_surgical
Macaca mulatta Primates Macaca_mulatta male surgical 0.418 0.011 77 male_surgical
Macaca nemestrina Primates Macaca_nemestrina male surgical 0.252 0.041 78 male_surgical
Macaca nigra Primates Macaca_nigra male surgical -0.417 0.020 79 male_surgical
Macaca silenus Primates Macaca_silenus male surgical 0.049 0.013 80 male_surgical
Macaca sylvanus Primates Macaca_sylvanus male surgical 0.323 0.012 81 male_surgical
Macaca tonkeana Primates Macaca_tonkeana male surgical 0.042 0.033 82 male_surgical
Macropus eugenii Diprotodontia Macropus_eugenii male surgical 0.403 0.038 83 male_surgical
Macropus fuliginosus Diprotodontia Macropus_fuliginosus male surgical 0.171 0.020 84 male_surgical
Macropus giganteus Diprotodontia Macropus_giganteus male surgical 0.820 0.016 85 male_surgical
Macropus parma Diprotodontia Macropus_parma male surgical 0.285 0.035 86 male_surgical
Macropus robustus Diprotodontia Macropus_robustus male surgical 0.053 0.027 87 male_surgical
Macropus rufogriseus Diprotodontia Macropus_rufogriseus male surgical 0.202 0.004 88 male_surgical
Macropus rufus Diprotodontia Macropus_rufus male surgical 0.206 0.004 89 male_surgical
Mephitis mephitis Carnivora Mephitis_mephitis male surgical 0.048 0.007 90 male_surgical
Mungos mungo Carnivora Mungos_mungo male surgical 0.003 0.032 91 male_surgical
Muntiacus reevesi Artiodactyla Muntiacus_reevesi male surgical 0.476 0.013 92 male_surgical
Mustela nigripes Carnivora Mustela_nigripes male surgical -0.045 0.003 93 male_surgical
Mustela putorius Carnivora Mustela_putorius male surgical -0.060 0.002 94 male_surgical
Myocastor coypus Rodentia Myocastor_coypus male surgical 0.112 0.045 95 male_surgical
Nasua narica Carnivora Nasua_narica male surgical -0.017 0.013 96 male_surgical
Nasua nasua Carnivora Nasua_nasua male surgical 0.129 0.006 97 male_surgical
Nyctereutes procyonoides Carnivora Nyctereutes_procyonoides male surgical -0.150 0.033 98 male_surgical
Octodon degus Rodentia Octodon_degus male surgical -0.060 0.012 99 male_surgical
Odocoileus virginianus Artiodactyla Odocoileus_virginianus male surgical 0.244 0.010 100 male_surgical
Oryctolagus cuniculus Lagomorpha Oryctolagus_cuniculus male surgical 0.109 0.002 101 male_surgical
Oryx dammah Artiodactyla Oryx_dammah male surgical 0.359 0.005 102 male_surgical
Oryx gazella Artiodactyla Oryx_gazella male surgical 0.340 0.014 103 male_surgical
Ovis aries Artiodactyla Ovis_aries male surgical 0.318 0.004 104 male_surgical
Ovis canadensis Artiodactyla Ovis_canadensis male surgical 0.438 0.017 105 male_surgical
Pan troglodytes Primates Pan_troglodytes male surgical 0.455 0.010 106 male_surgical
Panthera leo Carnivora Panthera_leo male surgical -0.132 0.003 107 male_surgical
Panthera pardus Carnivora Panthera_pardus male surgical -0.245 0.019 108 male_surgical
Panthera tigris Carnivora Panthera_tigris male surgical -0.140 0.003 109 male_surgical
Papio anubis Primates Papio_anubis male surgical 0.772 0.099 110 male_surgical
Papio hamadryas Primates Papio_hamadryas male surgical 0.363 0.004 111 male_surgical
Papio papio Primates Papio_papio male surgical -0.097 0.031 112 male_surgical
Pecari tajacu Artiodactyla Pecari_tajacu male surgical 0.551 0.009 113 male_surgical
Petaurus breviceps Diprotodontia Petaurus_breviceps male surgical -0.138 0.010 114 male_surgical
Petrogale xanthopus Diprotodontia Petrogale_xanthopus male surgical 0.427 0.012 115 male_surgical
Phacochoerus africanus Artiodactyla Phacochoerus_africanus male surgical 0.005 0.023 116 male_surgical
Phascolarctos cinereus Diprotodontia Phascolarctos_cinereus male surgical 0.811 0.026 117 male_surgical
Pithecia pithecia Primates Pithecia_pithecia male surgical 0.195 0.042 118 male_surgical
Potamochoerus porcus Artiodactyla Potamochoerus_porcus male surgical 0.112 0.015 119 male_surgical
Potos flavus Carnivora Potos_flavus male surgical 0.289 0.022 120 male_surgical
Procavia capensis Hyracoidea Procavia_capensis male surgical 0.060 0.021 121 male_surgical
Procyon lotor Carnivora Procyon_lotor male surgical 0.245 0.004 122 male_surgical
Puma concolor Carnivora Puma_concolor male surgical 0.168 0.003 123 male_surgical
Rangifer tarandus Artiodactyla Rangifer_tarandus male surgical 0.344 0.015 124 male_surgical
Rattus norvegicus Rodentia Rattus_norvegicus male surgical -0.023 0.005 125 male_surgical
Rousettus aegyptiacus Chiroptera Rousettus_aegyptiacus male surgical -0.429 0.005 126 male_surgical
Saguinus oedipus Primates Saguinus_oedipus male surgical 0.113 0.012 127 male_surgical
Saimiri boliviensis Primates Saimiri_boliviensis male surgical -0.175 0.020 128 male_surgical
Saimiri sciureus Primates Saimiri_sciureus male surgical 0.346 0.019 129 male_surgical
Sapajus apella Primates Sapajus_apella male surgical -0.044 0.010 130 male_surgical
Sapajus xanthosternos Primates Sapajus_xanthosternos male surgical 0.459 0.197 131 male_surgical
Suricata suricatta Carnivora Suricata_suricatta male surgical 0.013 0.002 132 male_surgical
Sus scrofa Artiodactyla Sus_scrofa male surgical 0.174 0.004 133 male_surgical
Tapirus terrestris Perissodactyla Tapirus_terrestris male surgical 0.195 0.066 134 male_surgical
Tragelaphus angasii Artiodactyla Tragelaphus_angasii male surgical 0.110 0.040 135 male_surgical
Tragelaphus oryx Artiodactyla Tragelaphus_oryx male surgical 0.142 0.004 136 male_surgical
Tragelaphus strepsiceros Artiodactyla Tragelaphus_strepsiceros male surgical -0.033 0.018 137 male_surgical
Ursus americanus Carnivora Ursus_americanus male surgical 0.081 0.005 138 male_surgical
Ursus arctos Carnivora Ursus_arctos male surgical 0.055 0.006 139 male_surgical
Varecia variegata Primates Varecia_variegata male surgical 0.116 0.010 140 male_surgical
Vicugna pacos Artiodactyla Vicugna_pacos male surgical 0.068 0.004 141 male_surgical
Vicugna vicugna Artiodactyla Vicugna_vicugna male surgical 0.204 0.057 142 male_surgical
Vulpes lagopus Carnivora Vulpes_lagopus male surgical 0.091 0.016 143 male_surgical
Vulpes vulpes Carnivora Vulpes_vulpes male surgical 0.155 0.011 144 male_surgical
Vulpes zerda Carnivora Vulpes_zerda male surgical -0.117 0.008 145 male_surgical
Wallabia bicolor Diprotodontia Wallabia_bicolor male surgical 1.184 0.073 146 male_surgical
Zalophus californianus Carnivora Zalophus_californianus male surgical 0.083 0.007 147 male_surgical
Ailurus fulgens Carnivora Ailurus_fulgens female hormonal -0.165 0.009 148 female_hormonal
Alouatta caraya Primates Alouatta_caraya female hormonal 0.445 0.014 149 female_hormonal
Aonyx cinerea Carnivora Aonyx_cinerea female hormonal 0.176 0.008 150 female_hormonal
Ateles fusciceps Primates Ateles_fusciceps female hormonal 0.247 0.132 151 female_hormonal
Ateles geoffroyi Primates Ateles_geoffroyi female hormonal 0.070 0.028 152 female_hormonal
Axis axis Artiodactyla Axis_axis female hormonal -0.091 0.017 153 female_hormonal
Callimico goeldii Primates Callimico_goeldii female hormonal -0.073 0.026 154 female_hormonal
Callithrix geoffroyi Primates Callithrix_geoffroyi female hormonal -0.069 0.017 155 female_hormonal
Callithrix jacchus Primates Callithrix_jacchus female hormonal 0.061 0.018 156 female_hormonal
Canis lupus Carnivora Canis_lupus female hormonal -0.340 0.011 157 female_hormonal
Capra hircus Artiodactyla Capra_hircus female hormonal -0.102 0.022 158 female_hormonal
Cebuella pygmaea Primates Cebuella_pygmaea female hormonal 0.250 0.049 159 female_hormonal
Cercopithecus neglectus Primates Cercopithecus_neglectus female hormonal 0.231 0.053 160 female_hormonal
Cervus canadensis Artiodactyla Cervus_canadensis female hormonal 0.009 0.011 161 female_hormonal
Colobus angolensis Primates Colobus_angolensis female hormonal 0.422 0.118 162 female_hormonal
Colobus guereza Primates Colobus_guereza female hormonal 0.463 0.011 163 female_hormonal
Erythrocebus patas Primates Erythrocebus_patas female hormonal 0.046 0.016 164 female_hormonal
Eulemur coronatus Primates Eulemur_coronatus female hormonal 0.331 0.012 165 female_hormonal
Eulemur macaco Primates Eulemur_macaco female hormonal 0.511 0.043 166 female_hormonal
Eulemur rubriventer Primates Eulemur_rubriventer female hormonal 0.035 0.094 167 female_hormonal
Giraffa camelopardalis Artiodactyla Giraffa_camelopardalis female hormonal 0.198 0.006 168 female_hormonal
Gorilla gorilla Primates Gorilla_gorilla female hormonal 0.359 0.021 169 female_hormonal
Hippopotamus amphibius Artiodactyla Hippopotamus_amphibius female hormonal 0.489 0.091 170 female_hormonal
Hydrochoerus hydrochaeris Rodentia Hydrochoerus_hydrochaeris female hormonal 0.015 0.034 171 female_hormonal
Hylobates lar Primates Hylobates_lar female hormonal 0.124 0.043 172 female_hormonal
Lemur catta Primates Lemur_catta female hormonal 0.189 0.004 173 female_hormonal
Leontopithecus chrysomelas Primates Leontopithecus_chrysomelas female hormonal 0.333 0.013 174 female_hormonal
Leontopithecus rosalia Primates Leontopithecus_rosalia female hormonal 0.149 0.008 175 female_hormonal
Lycaon pictus Carnivora Lycaon_pictus female hormonal -0.215 0.011 176 female_hormonal
Lynx lynx Carnivora Lynx_lynx female hormonal 0.153 0.027 177 female_hormonal
Macaca fascicularis Primates Macaca_fascicularis female hormonal -0.107 0.021 178 female_hormonal
Macaca fuscata Primates Macaca_fuscata female hormonal 0.100 0.006 179 female_hormonal
Macaca nigra Primates Macaca_nigra female hormonal -0.062 0.016 180 female_hormonal
Macaca silenus Primates Macaca_silenus female hormonal 0.061 0.020 181 female_hormonal
Macaca sylvanus Primates Macaca_sylvanus female hormonal 0.217 0.008 182 female_hormonal
Macaca tonkeana Primates Macaca_tonkeana female hormonal -0.435 0.051 183 female_hormonal
Macropus rufus Diprotodontia Macropus_rufus female hormonal -0.043 0.019 184 female_hormonal
Muntiacus reevesi Artiodactyla Muntiacus_reevesi female hormonal 0.084 0.022 185 female_hormonal
Mustela putorius Carnivora Mustela_putorius female hormonal -0.295 0.027 186 female_hormonal
Nasua nasua Carnivora Nasua_nasua female hormonal 0.009 0.020 187 female_hormonal
Octodon degus Rodentia Octodon_degus female hormonal 0.298 0.028 188 female_hormonal
Pan paniscus Primates Pan_paniscus female hormonal -0.406 0.438 189 female_hormonal
Pan troglodytes Primates Pan_troglodytes female hormonal 0.159 0.005 190 female_hormonal
Panthera leo Carnivora Panthera_leo female hormonal 0.169 0.002 191 female_hormonal
Panthera onca Carnivora Panthera_onca female hormonal 0.020 0.010 192 female_hormonal
Panthera pardus Carnivora Panthera_pardus female hormonal 0.023 0.019 193 female_hormonal
Panthera tigris Carnivora Panthera_tigris female hormonal -0.018 0.004 194 female_hormonal
Papio hamadryas Primates Papio_hamadryas female hormonal 0.276 0.002 195 female_hormonal
Papio papio Primates Papio_papio female hormonal -0.013 0.019 196 female_hormonal
Petrogale xanthopus Diprotodontia Petrogale_xanthopus female hormonal 0.057 0.020 197 female_hormonal
Phacochoerus africanus Artiodactyla Phacochoerus_africanus female hormonal 0.071 0.015 198 female_hormonal
Pithecia pithecia Primates Pithecia_pithecia female hormonal 0.457 0.027 199 female_hormonal
Pongo abelii Primates Pongo_abelii female hormonal 0.261 0.035 200 female_hormonal
Pongo pygmaeus Primates Pongo_pygmaeus female hormonal 0.339 0.030 201 female_hormonal
Potamochoerus porcus Artiodactyla Potamochoerus_porcus female hormonal -0.027 0.012 202 female_hormonal
Propithecus coquereli Primates Propithecus_coquereli female hormonal 0.744 0.046 203 female_hormonal
Pteropus rodricensis Chiroptera Pteropus_rodricensis female hormonal 0.174 0.016 204 female_hormonal
Saguinus bicolor Primates Saguinus_bicolor female hormonal 0.538 0.042 205 female_hormonal
Saguinus imperator Primates Saguinus_imperator female hormonal 0.202 0.011 206 female_hormonal
Saguinus oedipus Primates Saguinus_oedipus female hormonal 0.249 0.008 207 female_hormonal
Saimiri boliviensis Primates Saimiri_boliviensis female hormonal -0.217 0.039 208 female_hormonal
Saimiri sciureus Primates Saimiri_sciureus female hormonal 0.391 0.026 209 female_hormonal
Sapajus apella Primates Sapajus_apella female hormonal 0.680 0.062 210 female_hormonal
Sapajus xanthosternos Primates Sapajus_xanthosternos female hormonal 0.562 0.338 211 female_hormonal
Suricata suricatta Carnivora Suricata_suricatta female hormonal 0.127 0.004 212 female_hormonal
Symphalangus syndactylus Primates Symphalangus_syndactylus female hormonal 0.579 0.065 213 female_hormonal
Tapirus terrestris Perissodactyla Tapirus_terrestris female hormonal 0.132 0.033 214 female_hormonal
Theropithecus gelada Primates Theropithecus_gelada female hormonal 0.158 0.083 215 female_hormonal
Trachypithecus auratus Primates Trachypithecus_auratus female hormonal -0.255 0.042 216 female_hormonal
Trachypithecus cristatus Primates Trachypithecus_cristatus female hormonal 0.523 0.155 217 female_hormonal
Trachypithecus francoisi Primates Trachypithecus_francoisi female hormonal -0.005 0.040 218 female_hormonal
Tragelaphus strepsiceros Artiodactyla Tragelaphus_strepsiceros female hormonal -0.218 0.018 219 female_hormonal
Varecia rubra Primates Varecia_rubra female hormonal 0.142 0.007 220 female_hormonal
Varecia variegata Primates Varecia_variegata female hormonal 0.096 0.012 221 female_hormonal
Zalophus californianus Carnivora Zalophus_californianus female hormonal 0.060 0.035 222 female_hormonal
Canis latrans Carnivora Canis_latrans female surgical 0.238 0.011 223 female_surgical
Canis lupus Carnivora Canis_lupus female surgical 0.095 0.003 224 female_surgical
Cavia porcellus Rodentia Cavia_porcellus female surgical -0.243 0.014 225 female_surgical
Cynomys ludovicianus Rodentia Cynomys_ludovicianus female surgical -0.194 0.023 226 female_surgical
Eidolon helvum Chiroptera Eidolon_helvum female surgical 0.111 0.006 227 female_surgical
Felis catus Carnivora Felis_catus female surgical 0.226 0.004 228 female_surgical
Lemur catta Primates Lemur_catta female surgical -0.028 0.013 229 female_surgical
Leptailurus serval Carnivora Leptailurus_serval female surgical 0.065 0.021 230 female_surgical
Lycaon pictus Carnivora Lycaon_pictus female surgical -0.215 0.008 231 female_surgical
Lynx rufus Carnivora Lynx_rufus female surgical 0.078 0.004 232 female_surgical
Macaca fascicularis Primates Macaca_fascicularis female surgical 0.042 0.013 233 female_surgical
Macaca fuscata Primates Macaca_fuscata female surgical 0.510 0.016 234 female_surgical
Macaca mulatta Primates Macaca_mulatta female surgical 0.357 0.024 235 female_surgical
Mephitis mephitis Carnivora Mephitis_mephitis female surgical 0.284 0.010 236 female_surgical
Mustela nigripes Carnivora Mustela_nigripes female surgical -0.008 0.003 237 female_surgical
Mustela putorius Carnivora Mustela_putorius female surgical 0.157 0.003 238 female_surgical
Nasua nasua Carnivora Nasua_nasua female surgical 0.073 0.023 239 female_surgical
Oryctolagus cuniculus Lagomorpha Oryctolagus_cuniculus female surgical 0.313 0.004 240 female_surgical
Panthera leo Carnivora Panthera_leo female surgical 0.018 0.003 241 female_surgical
Panthera pardus Carnivora Panthera_pardus female surgical -0.082 0.012 242 female_surgical
Panthera tigris Carnivora Panthera_tigris female surgical -0.023 0.004 243 female_surgical
Papio hamadryas Primates Papio_hamadryas female surgical 0.255 0.003 244 female_surgical
Procyon lotor Carnivora Procyon_lotor female surgical 0.110 0.006 245 female_surgical
Puma concolor Carnivora Puma_concolor female surgical 0.158 0.004 246 female_surgical
Rattus norvegicus Rodentia Rattus_norvegicus female surgical 0.060 0.008 247 female_surgical
Saimiri sciureus Primates Saimiri_sciureus female surgical 0.166 0.038 248 female_surgical
Suricata suricatta Carnivora Suricata_suricatta female surgical -0.111 0.009 249 female_surgical
Sus scrofa Artiodactyla Sus_scrofa female surgical 0.151 0.012 250 female_surgical
Vulpes vulpes Carnivora Vulpes_vulpes female surgical 0.164 0.027 251 female_surgical
Giraffa camelopardalis Artiodactyla Giraffa_camelopardalis male immunological 0.282 0.057 252 male_immunological
Bison bison Artiodactyla Bison_bison female immunological 0.206 0.021 253 female_immunological
Giraffa camelopardalis Artiodactyla Giraffa_camelopardalis female immunological 0.133 0.009 254 female_immunological
Code
kable(dat_comb, "html", escape = FALSE, digits = 3) %>% kable_styling("striped", position = "left", full_width = TRUE) %>% 
  scroll_box(width = "100%", 
    height = "500px")
species phylogeny category yi vi obs_id contraception abs_yi abs_yi2 abs_vi
Alouatta caraya Alouatta_caraya F normal/M surgical -0.040 0.025 1 F normal/M contra. 0.040 0.130 0.010
Aonyx cinerea Aonyx_cinerea F normal/M surgical -0.033 0.006 2 F normal/M contra. 0.033 0.068 0.003
Ateles geoffroyi Ateles_geoffroyi F normal/M surgical 0.051 0.013 3 F normal/M contra. 0.051 0.101 0.006
Axis axis Axis_axis F normal/M surgical 0.572 0.057 4 F normal/M contra. 0.572 0.573 0.055
Bison bison Bison_bison F normal/M surgical -0.046 0.006 5 F normal/M contra. 0.046 0.074 0.003
Callithrix jacchus Callithrix_jacchus F normal/M surgical -0.367 0.017 6 F normal/M contra. 0.367 0.368 0.016
Canis latrans Canis_latrans F normal/M surgical -0.329 0.010 7 F normal/M contra. 0.329 0.329 0.010
Canis lupus Canis_lupus F normal/M surgical 0.021 0.002 8 F normal/M contra. 0.021 0.038 0.001
Capra hircus Capra_hircus F normal/M surgical -0.022 0.001 9 F normal/M contra. 0.022 0.026 0.000
Cavia porcellus Cavia_porcellus F normal/M surgical -0.106 0.006 10 F normal/M contra. 0.106 0.112 0.005
Cervus canadensis Cervus_canadensis F normal/M surgical -0.456 0.022 11 F normal/M contra. 0.456 0.457 0.022
Colobus guereza Colobus_guereza F normal/M surgical -0.017 0.016 12 F normal/M contra. 0.017 0.100 0.006
Cynomys ludovicianus Cynomys_ludovicianus F normal/M surgical 0.071 0.010 13 F normal/M contra. 0.071 0.097 0.005
Eidolon helvum Eidolon_helvum F normal/M surgical -0.191 0.005 14 F normal/M contra. 0.191 0.191 0.004
Erythrocebus patas Erythrocebus_patas F normal/M surgical -0.039 0.021 15 F normal/M contra. 0.039 0.121 0.008
Felis catus Felis_catus F normal/M surgical -0.339 0.006 16 F normal/M contra. 0.339 0.339 0.006
Giraffa camelopardalis Giraffa_camelopardalis F normal/M surgical -0.220 0.006 17 F normal/M contra. 0.220 0.220 0.006
Hydrochoerus hydrochaeris Hydrochoerus_hydrochaeris F normal/M surgical 0.050 0.008 18 F normal/M contra. 0.050 0.084 0.004
Lemur catta Lemur_catta F normal/M surgical -0.069 0.004 19 F normal/M contra. 0.069 0.078 0.003
Leptailurus serval Leptailurus_serval F normal/M surgical -0.148 0.010 20 F normal/M contra. 0.148 0.154 0.008
Lycaon pictus Lycaon_pictus F normal/M surgical 0.254 0.019 21 F normal/M contra. 0.254 0.257 0.017
Lynx lynx Lynx_lynx F normal/M surgical 0.136 0.006 22 F normal/M contra. 0.136 0.139 0.005
Lynx rufus Lynx_rufus F normal/M surgical -0.174 0.003 23 F normal/M contra. 0.174 0.175 0.003
Macaca fascicularis Macaca_fascicularis F normal/M surgical -0.130 0.043 24 F normal/M contra. 0.130 0.197 0.021
Macaca fuscata Macaca_fuscata F normal/M surgical -0.252 0.009 25 F normal/M contra. 0.252 0.252 0.009
Macaca mulatta Macaca_mulatta F normal/M surgical -0.418 0.010 26 F normal/M contra. 0.418 0.418 0.010
Macaca nigra Macaca_nigra F normal/M surgical 0.417 0.019 27 F normal/M contra. 0.417 0.418 0.019
Macaca silenus Macaca_silenus F normal/M surgical -0.049 0.013 28 F normal/M contra. 0.049 0.098 0.005
Macaca sylvanus Macaca_sylvanus F normal/M surgical -0.323 0.011 29 F normal/M contra. 0.323 0.323 0.011
Macaca tonkeana Macaca_tonkeana F normal/M surgical -0.042 0.038 30 F normal/M contra. 0.042 0.159 0.015
Macropus rufus Macropus_rufus F normal/M surgical -0.206 0.004 31 F normal/M contra. 0.206 0.206 0.004
Mephitis mephitis Mephitis_mephitis F normal/M surgical -0.048 0.007 32 F normal/M contra. 0.048 0.076 0.003
Muntiacus reevesi Muntiacus_reevesi F normal/M surgical -0.476 0.013 33 F normal/M contra. 0.476 0.476 0.013
Mustela nigripes Mustela_nigripes F normal/M surgical 0.045 0.003 34 F normal/M contra. 0.045 0.056 0.002
Mustela putorius Mustela_putorius F normal/M surgical 0.060 0.002 35 F normal/M contra. 0.060 0.066 0.002
Nasua nasua Nasua_nasua F normal/M surgical -0.129 0.006 36 F normal/M contra. 0.129 0.132 0.005
Octodon degus Octodon_degus F normal/M surgical 0.060 0.012 37 F normal/M contra. 0.060 0.101 0.006
Oryctolagus cuniculus Oryctolagus_cuniculus F normal/M surgical -0.109 0.002 38 F normal/M contra. 0.109 0.109 0.002
Pan troglodytes Pan_troglodytes F normal/M surgical -0.455 0.010 39 F normal/M contra. 0.455 0.455 0.010
Panthera leo Panthera_leo F normal/M surgical 0.132 0.003 40 F normal/M contra. 0.132 0.133 0.003
Panthera pardus Panthera_pardus F normal/M surgical 0.245 0.019 41 F normal/M contra. 0.245 0.249 0.017
Panthera tigris Panthera_tigris F normal/M surgical 0.140 0.003 42 F normal/M contra. 0.140 0.140 0.003
Papio hamadryas Papio_hamadryas F normal/M surgical -0.363 0.004 43 F normal/M contra. 0.363 0.363 0.004
Papio papio Papio_papio F normal/M surgical 0.097 0.032 44 F normal/M contra. 0.097 0.162 0.015
Petrogale xanthopus Petrogale_xanthopus F normal/M surgical -0.427 0.013 45 F normal/M contra. 0.427 0.427 0.013
Phacochoerus africanus Phacochoerus_africanus F normal/M surgical -0.005 0.023 46 F normal/M contra. 0.005 0.120 0.008
Pithecia pithecia Pithecia_pithecia F normal/M surgical -0.195 0.040 47 F normal/M contra. 0.195 0.231 0.025
Potamochoerus porcus Potamochoerus_porcus F normal/M surgical -0.112 0.015 48 F normal/M contra. 0.112 0.135 0.009
Procyon lotor Procyon_lotor F normal/M surgical -0.245 0.004 49 F normal/M contra. 0.245 0.245 0.004
Puma concolor Puma_concolor F normal/M surgical -0.168 0.003 50 F normal/M contra. 0.168 0.168 0.003
Rattus norvegicus Rattus_norvegicus F normal/M surgical 0.023 0.005 51 F normal/M contra. 0.023 0.059 0.002
Saguinus oedipus Saguinus_oedipus F normal/M surgical -0.113 0.012 52 F normal/M contra. 0.113 0.131 0.008
Saimiri boliviensis Saimiri_boliviensis F normal/M surgical 0.175 0.019 53 F normal/M contra. 0.175 0.189 0.014
Saimiri sciureus Saimiri_sciureus F normal/M surgical -0.346 0.019 54 F normal/M contra. 0.346 0.346 0.019
Sapajus apella Sapajus_apella F normal/M surgical 0.044 0.011 55 F normal/M contra. 0.044 0.090 0.005
Sapajus xanthosternos Sapajus_xanthosternos F normal/M surgical -0.459 0.273 56 F normal/M contra. 0.459 0.568 0.161
Suricata suricatta Suricata_suricatta F normal/M surgical -0.013 0.002 57 F normal/M contra. 0.013 0.039 0.001
Sus scrofa Sus_scrofa F normal/M surgical -0.174 0.004 58 F normal/M contra. 0.174 0.174 0.004
Tapirus terrestris Tapirus_terrestris F normal/M surgical -0.195 0.066 59 F normal/M contra. 0.195 0.262 0.036
Tragelaphus strepsiceros Tragelaphus_strepsiceros F normal/M surgical 0.033 0.018 60 F normal/M contra. 0.033 0.109 0.007
Varecia variegata Varecia_variegata F normal/M surgical -0.116 0.010 61 F normal/M contra. 0.116 0.129 0.007
Vulpes vulpes Vulpes_vulpes F normal/M surgical -0.155 0.011 62 F normal/M contra. 0.155 0.161 0.009
Zalophus californianus Zalophus_californianus F normal/M surgical -0.083 0.007 63 F normal/M contra. 0.083 0.096 0.004
Alouatta caraya Alouatta_caraya F hormonal/M normal 0.344 0.070 64 F contra./M normal 0.344 0.368 0.053
Aonyx cinerea Aonyx_cinerea F hormonal/M normal 0.033 0.100 65 F contra./M normal 0.033 0.253 0.037
Ateles geoffroyi Ateles_geoffroyi F hormonal/M normal -0.015 0.073 66 F contra./M normal 0.015 0.216 0.027
Axis axis Axis_axis F hormonal/M normal -0.335 13.495 67 F contra./M normal 0.335 2.943 4.944
Callithrix jacchus Callithrix_jacchus F hormonal/M normal -0.050 0.267 68 F contra./M normal 0.050 0.415 0.098
Canis lupus Canis_lupus F hormonal/M normal -0.377 0.114 69 F contra./M normal 0.377 0.422 0.078
Capra hircus Capra_hircus F hormonal/M normal -0.067 0.358 70 F contra./M normal 0.067 0.481 0.132
Cervus canadensis Cervus_canadensis F hormonal/M normal 0.410 0.297 71 F contra./M normal 0.410 0.552 0.160
Colobus guereza Colobus_guereza F hormonal/M normal 0.098 0.122 72 F contra./M normal 0.098 0.289 0.048
Erythrocebus patas Erythrocebus_patas F hormonal/M normal 0.281 0.165 73 F contra./M normal 0.281 0.398 0.085
Giraffa camelopardalis Giraffa_camelopardalis F hormonal/M normal 0.471 0.142 74 F contra./M normal 0.471 0.509 0.104
Hydrochoerus hydrochaeris Hydrochoerus_hydrochaeris F hormonal/M normal 0.051 0.471 75 F contra./M normal 0.051 0.549 0.172
Lemur catta Lemur_catta F hormonal/M normal 0.083 0.130 76 F contra./M normal 0.083 0.296 0.050
Lycaon pictus Lycaon_pictus F hormonal/M normal -0.338 0.119 77 F contra./M normal 0.338 0.398 0.075
Lynx lynx Lynx_lynx F hormonal/M normal 0.116 0.058 78 F contra./M normal 0.116 0.214 0.026
Macaca fascicularis Macaca_fascicularis F hormonal/M normal 0.361 0.273 79 F contra./M normal 0.361 0.513 0.141
Macaca fuscata Macaca_fuscata F hormonal/M normal 0.308 0.128 80 F contra./M normal 0.308 0.386 0.075
Macaca nigra Macaca_nigra F hormonal/M normal 0.001 0.149 81 F contra./M normal 0.001 0.308 0.054
Macaca silenus Macaca_silenus F hormonal/M normal 0.243 0.070 82 F contra./M normal 0.243 0.294 0.042
Macaca sylvanus Macaca_sylvanus F hormonal/M normal 0.353 0.202 83 F contra./M normal 0.353 0.464 0.112
Macaca tonkeana Macaca_tonkeana F hormonal/M normal -0.253 0.072 84 F contra./M normal 0.253 0.303 0.044
Macropus rufus Macropus_rufus F hormonal/M normal 0.213 0.388 85 F contra./M normal 0.213 0.526 0.157
Muntiacus reevesi Muntiacus_reevesi F hormonal/M normal 0.172 0.266 86 F contra./M normal 0.172 0.434 0.107
Mustela putorius Mustela_putorius F hormonal/M normal -0.236 0.225 87 F contra./M normal 0.236 0.424 0.100
Nasua nasua Nasua_nasua F hormonal/M normal 0.096 0.232 88 F contra./M normal 0.096 0.392 0.087
Octodon degus Octodon_degus F hormonal/M normal 0.482 0.455 89 F contra./M normal 0.482 0.670 0.238
Pan troglodytes Pan_troglodytes F hormonal/M normal 0.348 0.084 90 F contra./M normal 0.348 0.381 0.061
Panthera leo Panthera_leo F hormonal/M normal 0.088 0.084 91 F contra./M normal 0.088 0.242 0.033
Panthera pardus Panthera_pardus F hormonal/M normal -0.026 0.069 92 F contra./M normal 0.026 0.210 0.025
Panthera tigris Panthera_tigris F hormonal/M normal -0.023 0.067 93 F contra./M normal 0.023 0.207 0.024
Papio hamadryas Papio_hamadryas F hormonal/M normal 0.480 0.133 94 F contra./M normal 0.480 0.512 0.101
Papio papio Papio_papio F hormonal/M normal 0.230 0.111 95 F contra./M normal 0.230 0.327 0.057
Petrogale xanthopus Petrogale_xanthopus F hormonal/M normal 0.408 0.447 96 F contra./M normal 0.408 0.630 0.217
Phacochoerus africanus Phacochoerus_africanus F hormonal/M normal 0.166 0.120 97 F contra./M normal 0.166 0.307 0.053
Pithecia pithecia Pithecia_pithecia F hormonal/M normal 0.153 0.187 98 F contra./M normal 0.153 0.367 0.076
Potamochoerus porcus Potamochoerus_porcus F hormonal/M normal -0.046 0.108 99 F contra./M normal 0.046 0.265 0.040
Saguinus imperator Saguinus_imperator F hormonal/M normal 0.054 0.128 100 F contra./M normal 0.054 0.288 0.047
Saguinus oedipus Saguinus_oedipus F hormonal/M normal 0.148 0.132 101 F contra./M normal 0.148 0.314 0.056
Saimiri boliviensis Saimiri_boliviensis F hormonal/M normal -0.170 0.242 102 F contra./M normal 0.170 0.416 0.098
Saimiri sciureus Saimiri_sciureus F hormonal/M normal 0.530 0.302 103 F contra./M normal 0.530 0.628 0.188
Sapajus apella Sapajus_apella F hormonal/M normal 0.744 0.064 104 F contra./M normal 0.744 0.744 0.064
Sapajus xanthosternos Sapajus_xanthosternos F hormonal/M normal 0.740 0.274 105 F contra./M normal 0.740 0.777 0.217
Suricata suricatta Suricata_suricatta F hormonal/M normal 0.073 0.097 106 F contra./M normal 0.073 0.255 0.037
Tapirus terrestris Tapirus_terrestris F hormonal/M normal 0.151 0.103 107 F contra./M normal 0.151 0.284 0.045
Tragelaphus strepsiceros Tragelaphus_strepsiceros F hormonal/M normal 0.180 0.373 108 F contra./M normal 0.180 0.508 0.147
Varecia variegata Varecia_variegata F hormonal/M normal 0.084 0.062 109 F contra./M normal 0.084 0.209 0.025
Zalophus californianus Zalophus_californianus F hormonal/M normal 0.210 0.081 110 F contra./M normal 0.210 0.286 0.043
Canis latrans Canis_latrans F hormonal/M normal 0.370 0.011 111 F contra./M normal 0.370 0.370 0.011
Canis lupus Canis_lupus F hormonal/M normal 0.058 0.005 112 F contra./M normal 0.058 0.073 0.003
Cavia porcellus Cavia_porcellus F hormonal/M normal -0.138 0.035 113 F contra./M normal 0.138 0.188 0.019
Cynomys ludovicianus Cynomys_ludovicianus F hormonal/M normal -0.127 0.033 114 F contra./M normal 0.127 0.179 0.017
Eidolon helvum Eidolon_helvum F hormonal/M normal 0.302 0.005 115 F contra./M normal 0.302 0.302 0.005
Felis catus Felis_catus F hormonal/M normal 0.520 0.006 116 F contra./M normal 0.520 0.520 0.006
Lemur catta Lemur_catta F hormonal/M normal -0.134 0.008 117 F contra./M normal 0.134 0.139 0.007
Leptailurus serval Leptailurus_serval F hormonal/M normal 0.106 0.011 118 F contra./M normal 0.106 0.124 0.007
Lycaon pictus Lycaon_pictus F hormonal/M normal -0.338 0.015 119 F contra./M normal 0.338 0.338 0.015
Lynx rufus Lynx_rufus F hormonal/M normal 0.194 0.004 120 F contra./M normal 0.194 0.194 0.004
Macaca fascicularis Macaca_fascicularis F hormonal/M normal 0.511 0.008 121 F contra./M normal 0.511 0.511 0.008
Macaca fuscata Macaca_fuscata F hormonal/M normal 0.718 0.006 122 F contra./M normal 0.718 0.718 0.006
Macaca mulatta Macaca_mulatta F hormonal/M normal 0.597 0.008 123 F contra./M normal 0.597 0.597 0.008
Mephitis mephitis Mephitis_mephitis F hormonal/M normal 0.305 0.014 124 F contra./M normal 0.305 0.305 0.014
Mustela nigripes Mustela_nigripes F hormonal/M normal 0.123 0.010 125 F contra./M normal 0.123 0.134 0.007
Mustela putorius Mustela_putorius F hormonal/M normal 0.216 0.009 126 F contra./M normal 0.216 0.217 0.009
Nasua nasua Nasua_nasua F hormonal/M normal 0.160 0.016 127 F contra./M normal 0.160 0.172 0.012
Oryctolagus cuniculus Oryctolagus_cuniculus F hormonal/M normal 0.175 0.009 128 F contra./M normal 0.175 0.178 0.009
Panthera leo Panthera_leo F hormonal/M normal -0.063 0.004 129 F contra./M normal 0.063 0.074 0.003
Panthera pardus Panthera_pardus F hormonal/M normal -0.131 0.009 130 F contra./M normal 0.131 0.138 0.007
Panthera tigris Panthera_tigris F hormonal/M normal -0.028 0.005 131 F contra./M normal 0.028 0.061 0.002
Papio hamadryas Papio_hamadryas F hormonal/M normal 0.459 0.003 132 F contra./M normal 0.459 0.459 0.003
Procyon lotor Procyon_lotor F hormonal/M normal 0.262 0.007 133 F contra./M normal 0.262 0.262 0.007
Puma concolor Puma_concolor F hormonal/M normal 0.250 0.004 134 F contra./M normal 0.250 0.250 0.004
Rattus norvegicus Rattus_norvegicus F hormonal/M normal 0.114 0.043 135 F contra./M normal 0.114 0.190 0.020
Saimiri sciureus Saimiri_sciureus F hormonal/M normal 0.306 0.015 136 F contra./M normal 0.306 0.306 0.015
Suricata suricatta Suricata_suricatta F hormonal/M normal -0.165 0.013 137 F contra./M normal 0.165 0.173 0.011
Sus scrofa Sus_scrofa F hormonal/M normal 0.165 0.011 138 F contra./M normal 0.165 0.170 0.009
Vulpes vulpes Vulpes_vulpes F hormonal/M normal 0.220 0.015 139 F contra./M normal 0.220 0.224 0.014
Canis latrans Canis_latrans F surgical/M surgical 0.041 0.015 140 F contra./M contra. 0.041 0.102 0.006
Canis lupus Canis_lupus F surgical/M surgical 0.078 0.006 141 F contra./M contra. 0.078 0.091 0.004
Cavia porcellus Cavia_porcellus F surgical/M surgical -0.244 0.040 142 F contra./M contra. 0.244 0.266 0.029
Cynomys ludovicianus Cynomys_ludovicianus F surgical/M surgical -0.056 0.041 143 F contra./M contra. 0.056 0.167 0.016
Eidolon helvum Eidolon_helvum F surgical/M surgical 0.112 0.007 144 F contra./M contra. 0.112 0.118 0.005
Felis catus Felis_catus F surgical/M surgical 0.180 0.008 145 F contra./M contra. 0.180 0.182 0.008
Lemur catta Lemur_catta F surgical/M surgical -0.202 0.012 146 F contra./M contra. 0.202 0.205 0.011
Leptailurus serval Leptailurus_serval F surgical/M surgical -0.042 0.019 147 F contra./M contra. 0.042 0.114 0.007
Lycaon pictus Lycaon_pictus F surgical/M surgical -0.084 0.033 148 F contra./M contra. 0.084 0.159 0.014
Lynx rufus Lynx_rufus F surgical/M surgical 0.020 0.006 149 F contra./M contra. 0.020 0.062 0.002
Macaca fascicularis Macaca_fascicularis F surgical/M surgical 0.381 0.044 150 F contra./M contra. 0.381 0.387 0.040
Macaca fuscata Macaca_fuscata F surgical/M surgical 0.466 0.012 151 F contra./M contra. 0.466 0.466 0.012
Macaca mulatta Macaca_mulatta F surgical/M surgical 0.179 0.014 152 F contra./M contra. 0.179 0.186 0.012
Mephitis mephitis Mephitis_mephitis F surgical/M surgical 0.257 0.019 153 F contra./M contra. 0.257 0.260 0.017
Mustela nigripes Mustela_nigripes F surgical/M surgical 0.168 0.012 154 F contra./M contra. 0.168 0.174 0.010
Mustela putorius Mustela_putorius F surgical/M surgical 0.276 0.010 155 F contra./M contra. 0.276 0.276 0.010
Nasua nasua Nasua_nasua F surgical/M surgical 0.030 0.020 156 F contra./M contra. 0.030 0.115 0.008
Oryctolagus cuniculus Oryctolagus_cuniculus F surgical/M surgical 0.067 0.011 157 F contra./M contra. 0.067 0.100 0.005
Panthera leo Panthera_leo F surgical/M surgical 0.070 0.007 158 F contra./M contra. 0.070 0.088 0.004
Panthera pardus Panthera_pardus F surgical/M surgical 0.114 0.026 159 F contra./M contra. 0.114 0.160 0.014
Panthera tigris Panthera_tigris F surgical/M surgical 0.112 0.008 160 F contra./M contra. 0.112 0.121 0.006
Papio hamadryas Papio_hamadryas F surgical/M surgical 0.096 0.006 161 F contra./M contra. 0.096 0.104 0.004
Procyon lotor Procyon_lotor F surgical/M surgical 0.017 0.010 162 F contra./M contra. 0.017 0.080 0.004
Puma concolor Puma_concolor F surgical/M surgical 0.082 0.006 163 F contra./M contra. 0.082 0.095 0.004
Rattus norvegicus Rattus_norvegicus F surgical/M surgical 0.137 0.047 164 F contra./M contra. 0.137 0.206 0.023
Saimiri sciureus Saimiri_sciureus F surgical/M surgical -0.040 0.033 165 F contra./M contra. 0.040 0.148 0.013
Suricata suricatta Suricata_suricatta F surgical/M surgical -0.178 0.015 166 F contra./M contra. 0.178 0.186 0.012
Sus scrofa Sus_scrofa F surgical/M surgical -0.010 0.014 167 F contra./M contra. 0.010 0.093 0.005
Vulpes vulpes Vulpes_vulpes F surgical/M surgical 0.065 0.025 168 F contra./M contra. 0.065 0.135 0.010
Alouatta caraya Alouatta_caraya F normal/M normal -0.101 0.008 169 F normal/M normal 0.101 0.113 0.006
Aonyx cinerea Aonyx_cinerea F normal/M normal -0.143 0.004 170 F normal/M normal 0.143 0.144 0.004
Ateles geoffroyi Ateles_geoffroyi F normal/M normal -0.085 0.004 171 F normal/M normal 0.085 0.089 0.003
Axis axis Axis_axis F normal/M normal -0.244 0.017 172 F normal/M normal 0.244 0.247 0.016
Bison bison Bison_bison F normal/M normal 0.230 0.003 173 F normal/M normal 0.230 0.230 0.003
Callithrix jacchus Callithrix_jacchus F normal/M normal -0.111 0.007 174 F normal/M normal 0.111 0.117 0.005
Canis latrans Canis_latrans F normal/M normal 0.131 0.012 175 F normal/M normal 0.131 0.144 0.009
Canis lupus Canis_lupus F normal/M normal -0.038 0.003 176 F normal/M normal 0.038 0.052 0.001
Capra hircus Capra_hircus F normal/M normal 0.035 0.002 177 F normal/M normal 0.035 0.048 0.001
Cavia porcellus Cavia_porcellus F normal/M normal 0.105 0.009 178 F normal/M normal 0.105 0.117 0.006
Cervus canadensis Cervus_canadensis F normal/M normal 0.401 0.005 179 F normal/M normal 0.401 0.401 0.005
Colobus guereza Colobus_guereza F normal/M normal -0.366 0.006 180 F normal/M normal 0.366 0.366 0.006
Cynomys ludovicianus Cynomys_ludovicianus F normal/M normal 0.067 0.011 181 F normal/M normal 0.067 0.101 0.006
Eidolon helvum Eidolon_helvum F normal/M normal 0.191 0.004 182 F normal/M normal 0.191 0.191 0.004
Erythrocebus patas Erythrocebus_patas F normal/M normal 0.235 0.007 183 F normal/M normal 0.235 0.236 0.007
Felis catus Felis_catus F normal/M normal 0.293 0.007 184 F normal/M normal 0.293 0.293 0.007
Giraffa camelopardalis Giraffa_camelopardalis F normal/M normal 0.273 0.003 185 F normal/M normal 0.273 0.273 0.003
Hydrochoerus hydrochaeris Hydrochoerus_hydrochaeris F normal/M normal 0.036 0.009 186 F normal/M normal 0.036 0.079 0.004
Lemur catta Lemur_catta F normal/M normal -0.106 0.002 187 F normal/M normal 0.106 0.107 0.002
Leptailurus serval Leptailurus_serval F normal/M normal 0.042 0.005 188 F normal/M normal 0.042 0.067 0.002
Lycaon pictus Lycaon_pictus F normal/M normal -0.123 0.006 189 F normal/M normal 0.123 0.127 0.005
Lynx lynx Lynx_lynx F normal/M normal -0.036 0.003 190 F normal/M normal 0.036 0.055 0.002
Lynx rufus Lynx_rufus F normal/M normal 0.116 0.003 191 F normal/M normal 0.116 0.117 0.003
Macaca fascicularis Macaca_fascicularis F normal/M normal 0.468 0.006 192 F normal/M normal 0.468 0.468 0.006
Macaca fuscata Macaca_fuscata F normal/M normal 0.208 0.004 193 F normal/M normal 0.208 0.208 0.004
Macaca mulatta Macaca_mulatta F normal/M normal 0.240 0.005 194 F normal/M normal 0.240 0.240 0.005
Macaca nigra Macaca_nigra F normal/M normal 0.064 0.009 195 F normal/M normal 0.064 0.091 0.004
Macaca silenus Macaca_silenus F normal/M normal 0.182 0.005 196 F normal/M normal 0.182 0.182 0.005
Macaca sylvanus Macaca_sylvanus F normal/M normal 0.136 0.008 197 F normal/M normal 0.136 0.141 0.006
Macaca tonkeana Macaca_tonkeana F normal/M normal 0.183 0.013 198 F normal/M normal 0.183 0.188 0.011
Macropus rufus Macropus_rufus F normal/M normal 0.256 0.006 199 F normal/M normal 0.256 0.256 0.006
Mephitis mephitis Mephitis_mephitis F normal/M normal 0.021 0.011 200 F normal/M normal 0.021 0.085 0.004
Muntiacus reevesi Muntiacus_reevesi F normal/M normal 0.088 0.006 201 F normal/M normal 0.088 0.098 0.004
Mustela nigripes Mustela_nigripes F normal/M normal 0.132 0.008 202 F normal/M normal 0.132 0.137 0.007
Mustela putorius Mustela_putorius F normal/M normal 0.059 0.008 203 F normal/M normal 0.059 0.087 0.004
Nasua nasua Nasua_nasua F normal/M normal 0.086 0.005 204 F normal/M normal 0.086 0.095 0.004
Octodon degus Octodon_degus F normal/M normal 0.183 0.024 205 F normal/M normal 0.183 0.201 0.017
Oryctolagus cuniculus Oryctolagus_cuniculus F normal/M normal -0.138 0.008 206 F normal/M normal 0.138 0.143 0.007
Pan troglodytes Pan_troglodytes F normal/M normal 0.189 0.002 207 F normal/M normal 0.189 0.189 0.002
Panthera leo Panthera_leo F normal/M normal -0.080 0.002 208 F normal/M normal 0.080 0.082 0.002
Panthera pardus Panthera_pardus F normal/M normal -0.049 0.003 209 F normal/M normal 0.049 0.059 0.002
Panthera tigris Panthera_tigris F normal/M normal -0.005 0.002 210 F normal/M normal 0.005 0.037 0.001
Papio hamadryas Papio_hamadryas F normal/M normal 0.204 0.004 211 F normal/M normal 0.204 0.204 0.004
Papio papio Papio_papio F normal/M normal 0.243 0.007 212 F normal/M normal 0.243 0.243 0.007
Petrogale xanthopus Petrogale_xanthopus F normal/M normal 0.351 0.016 213 F normal/M normal 0.351 0.351 0.016
Phacochoerus africanus Phacochoerus_africanus F normal/M normal 0.095 0.008 214 F normal/M normal 0.095 0.108 0.005
Pithecia pithecia Pithecia_pithecia F normal/M normal -0.304 0.010 215 F normal/M normal 0.304 0.304 0.010
Potamochoerus porcus Potamochoerus_porcus F normal/M normal -0.019 0.007 216 F normal/M normal 0.019 0.069 0.003
Procyon lotor Procyon_lotor F normal/M normal 0.152 0.005 217 F normal/M normal 0.152 0.153 0.005
Puma concolor Puma_concolor F normal/M normal 0.092 0.003 218 F normal/M normal 0.092 0.095 0.003
Rattus norvegicus Rattus_norvegicus F normal/M normal 0.054 0.024 219 F normal/M normal 0.054 0.132 0.010
Saguinus imperator Saguinus_imperator F normal/M normal -0.148 0.008 220 F normal/M normal 0.148 0.151 0.007
Saguinus oedipus Saguinus_oedipus F normal/M normal -0.101 0.004 221 F normal/M normal 0.101 0.104 0.004
Saimiri boliviensis Saimiri_boliviensis F normal/M normal 0.048 0.005 222 F normal/M normal 0.048 0.070 0.003
Saimiri sciureus Saimiri_sciureus F normal/M normal 0.139 0.005 223 F normal/M normal 0.139 0.141 0.004
Sapajus apella Sapajus_apella F normal/M normal 0.064 0.003 224 F normal/M normal 0.064 0.069 0.002
Sapajus xanthosternos Sapajus_xanthosternos F normal/M normal 0.178 0.022 225 F normal/M normal 0.178 0.195 0.016
Suricata suricatta Suricata_suricatta F normal/M normal -0.054 0.003 226 F normal/M normal 0.054 0.063 0.002
Sus scrofa Sus_scrofa F normal/M normal 0.014 0.005 227 F normal/M normal 0.014 0.056 0.002
Tapirus terrestris Tapirus_terrestris F normal/M normal 0.019 0.005 228 F normal/M normal 0.019 0.061 0.002
Tragelaphus strepsiceros Tragelaphus_strepsiceros F normal/M normal 0.398 0.008 229 F normal/M normal 0.398 0.398 0.008
Varecia variegata Varecia_variegata F normal/M normal -0.012 0.003 230 F normal/M normal 0.012 0.045 0.001
Vulpes vulpes Vulpes_vulpes F normal/M normal 0.055 0.006 231 F normal/M normal 0.055 0.078 0.003
Zalophus californianus Zalophus_californianus F normal/M normal 0.150 0.003 232 F normal/M normal 0.150 0.150 0.003
Aonyx cinerea Aonyx_cinerea F normal/M hornomal -0.280 0.028 233 NA 0.280 0.287 0.024
Lemur catta Lemur_catta F normal/M hornomal 0.032 0.068 234 NA 0.032 0.209 0.025
Lycaon pictus Lycaon_pictus F normal/M hornomal -0.200 0.010 235 NA 0.200 0.202 0.009
Saguinus imperator Saguinus_imperator F normal/M hornomal -0.166 0.042 236 NA 0.166 0.214 0.023
Saguinus oedipus Saguinus_oedipus F normal/M hornomal -0.298 0.061 237 NA 0.298 0.325 0.044
Suricata suricatta Suricata_suricatta F normal/M hornomal -0.030 0.025 238 NA 0.030 0.129 0.009
Giraffa camelopardalis Giraffa_camelopardalis F normal/M immunological -0.009 0.057 239 F normal/M contra. 0.009 0.191 0.021
Bison bison Bison_bison F immunological/M normal 0.436 0.008 240 F contra./M normal 0.436 0.436 0.008
Giraffa camelopardalis Giraffa_camelopardalis F immunological/M normal 0.406 0.006 241 F contra./M normal 0.406 0.406 0.006
Aonyx cinerea Aonyx_cinerea F hornomal/M hornomal -0.104 0.033 242 F contra./M contra. 0.104 0.169 0.016
Lemur catta Lemur_catta F hornomal/M hornomal 0.221 0.070 243 F contra./M contra. 0.221 0.281 0.040
Lycaon pictus Lycaon_pictus F hornomal/M hornomal -0.416 0.024 244 F contra./M contra. 0.416 0.416 0.024
Saguinus imperator Saguinus_imperator F hornomal/M hornomal 0.036 0.049 245 F contra./M contra. 0.036 0.179 0.018
Saguinus oedipus Saguinus_oedipus F hornomal/M hornomal -0.049 0.066 246 F contra./M contra. 0.049 0.209 0.025
Suricata suricatta Suricata_suricatta F hornomal/M hornomal 0.097 0.030 247 F contra./M contra. 0.097 0.160 0.014
Giraffa camelopardalis Giraffa_camelopardalis F immunological/M immunological 0.124 0.056 248 F contra./M contra. 0.124 0.215 0.026
Code
kable(dat_pre, "html", escape = FALSE, digits = 3) %>% kable_styling("striped", position = "left", full_width = TRUE) %>% 
  scroll_box(width = "100%", 
    height = "500px")
F_normal_m F_normal_sd F_normal_n F_hormonal_m F_hormonal_sd F_hormonal_n species phylogeny yi vi
11.613 8.408 2839 13.117 7.069 55 Panthera leo Panthera_leo 0.122 0.005
7.882 8.161 1897 10.593 8.272 46 Saguinus oedipus Saguinus_oedipus 0.296 0.014
11.094 7.029 3299 8.721 5.739 38 Panthera tigris Panthera_tigris -0.241 0.012
14.959 12.641 1406 17.399 11.606 123 Papio hamadryas Papio_hamadryas 0.151 0.004
28.159 24.501 1567 33.842 25.747 77 Pan troglodytes Pan_troglodytes 0.184 0.008
15.947 11.642 1037 21.239 11.010 46 Macaca fuscata Macaca_fuscata 0.287 0.006
9.581 9.854 3101 10.575 5.603 35 Axis axis Axis_axis 0.099 0.008
6.216 4.590 874 6.183 3.726 45 Lycaon pictus Lycaon_pictus -0.005 0.009
8.935 9.466 952 11.396 9.328 35 Colobus guereza Colobus_guereza 0.243 0.020
Code
kable(dat_post, "html", escape = FALSE, digits = 3) %>% kable_styling("striped", position = "left", full_width = TRUE) %>% 
  scroll_box(width = "100%", 
    height = "500px")
F_normal_m F_normal_sd F_normal_n F_hormonal_m F_hormonal_sd F_hormonal_n species phylogeny yi vi
7.185 8.618 1462 6.711 8.643 141 Callithrix jacchus Callithrix_jacchus -0.068 0.013
12.164 38.553 251 21.807 57.230 48 Pithecia pithecia Pithecia_pithecia 0.584 0.184
13.879 26.963 496 14.986 18.250 74 Varecia variegata Varecia_variegata 0.077 0.028
15.483 162.892 3131 20.721 113.894 305 Lemur catta Lemur_catta 0.291 0.134
9.111 11.046 1412 12.540 11.343 82 Aonyx cinereus Aonyx_cinerea 0.319 0.011
16.740 132.618 1453 18.573 55.852 106 Giraffa camelopardalis Giraffa_camelopardalis 0.104 0.129
7.907 7.615 4023 9.457 7.258 196 Suricata suricatta Suricata_suricatta 0.179 0.003
23.300 119.368 215 27.676 81.544 42 Macaca silenus Macaca_silenus 0.172 0.329
9.684 12.226 394 9.620 10.575 34 Callimico goeldii Callimico_goeldii -0.007 0.040
43.570 212.732 370 40.350 117.608 59 Macaca fuscata Macaca_fuscata -0.077 0.208
9.638 15.920 299 11.857 16.026 48 Leontopithecus chrysomelas Leontopithecus_chrysomelas 0.207 0.047
13.303 19.121 1986 16.417 19.999 327 Panthera leo Panthera_leo 0.210 0.006
9.024 9.050 2606 8.562 9.361 120 Canis lupus Canis_lupus -0.053 0.010
15.893 80.286 1031 23.421 78.259 144 Papio hamadryas Papio_hamadryas 0.388 0.102
11.057 34.509 375 33.182 112.981 72 Colobus guereza Colobus_guereza 1.099 0.187
31.079 39.490 351 35.932 25.712 139 Pan troglodytes Pan_troglodytes 0.145 0.008
15.816 60.105 116 21.564 74.521 46 Alouatta caraya Alouatta_caraya 0.310 0.384
6.336 5.835 627 6.804 6.038 70 Lycaon pictus Lycaon_pictus 0.071 0.013
13.564 39.306 379 18.027 47.137 168 Macaca sylvanus Macaca_sylvanus 0.284 0.063
8.934 15.214 253 11.405 18.944 100 Leontopithecus rosalia Leontopithecus_rosalia 0.244 0.039
10.949 13.225 1271 13.480 14.253 48 Saimiri sciureus Saimiri_sciureus 0.208 0.024
7.328 9.152 548 8.422 8.707 59 Saguinus imperator Saguinus_imperator 0.139 0.021
70.040 510.549 244 55.634 191.580 46 Pongo pygmaeus Pongo_pygmaeus -0.230 0.476
7.080 12.195 473 5.781 6.568 50 Callithrix geoffroyi Callithrix_geoffroyi -0.203 0.032
12.317 16.429 1669 14.434 13.064 97 Panthera tigris Panthera_tigris 0.159 0.010
19.021 112.556 123 25.227 127.771 93 Gorilla gorilla Gorilla_gorilla 0.282 0.561
4.502 3.806 477 5.535 4.069 85 Octodon degus Octodon_degus 0.207 0.008
8.589 9.015 604 8.760 5.664 38 Potamochoerus porcus Potamochoerus_porcus 0.020 0.013
14.283 40.089 602 13.305 15.088 36 Lynx lynx Lynx_lynx -0.071 0.049
9.588 17.631 133 15.719 30.151 44 Saguinus bicolor Saguinus_bicolor 0.494 0.109
6.446 7.381 1073 7.592 7.647 35 Cebuella pygmaea Cebuella_pygmaea 0.164 0.030
21.398 58.064 55 26.616 66.777 37 Sapajus xanthosternos Sapajus_xanthosternos 0.218 0.304
5.376 3.329 870 4.387 2.795 38 Mustela putorius Mustela_putorius -0.203 0.011
14.494 49.028 308 16.031 30.557 35 Tapirus terrestris Tapirus_terrestris 0.101 0.141
14.026 29.057 36 19.518 48.277 30 Trachypithecus cristatus Trachypithecus_cristatus 0.330 0.323
39.600 393.452 755 26.277 92.139 111 Macaca fascicularis Macaca_fascicularis -0.410 0.242
21.868 105.906 352 30.448 104.140 70 Varecia rubra Varecia_rubra 0.331 0.234
9.388 25.472 666 13.959 30.776 102 Pteropus rodricensis Pteropus_rodricensis 0.397 0.059
7.882 6.337 1144 10.593 13.636 125 Saguinus oedipus Saguinus_oedipus 0.296 0.014
24.073 109.790 106 33.005 123.388 33 Symphalangus syndactylus Symphalangus_syndactylus 0.316 0.620
9.984 11.060 763 8.851 7.122 55 Ailurus fulgens Ailurus_fulgens -0.120 0.013
8.505 9.477 373 9.594 5.980 40 Phacochoerus africanus Phacochoerus_africanus 0.121 0.013
5.617 5.716 2032 5.426 3.530 33 Hydrochoerus hydrochaeris Hydrochoerus_hydrochaeris -0.035 0.013
6.800 7.081 650 6.533 4.161 35 Petrogale xanthopus Petrogale_xanthopus -0.040 0.013
9.075 7.047 1415 10.281 5.600 33 Nasua nasua Nasua_nasua 0.125 0.009
Code
kable(dat_pre_post, "html", escape = FALSE, digits = 3) %>% kable_styling("striped", position = "left", full_width = TRUE) %>% 
  scroll_box(width = "100%", 
    height = "500px")
species phylogeny yi vi obs_id timing
Panthera leo Panthera_leo 0.122 0.005 1 Pre-2005
Saguinus oedipus Saguinus_oedipus 0.296 0.014 2 Pre-2005
Panthera tigris Panthera_tigris -0.241 0.012 3 Pre-2005
Papio hamadryas Papio_hamadryas 0.151 0.004 4 Pre-2005
Pan troglodytes Pan_troglodytes 0.184 0.008 5 Pre-2005
Macaca fuscata Macaca_fuscata 0.287 0.006 6 Pre-2005
Axis axis Axis_axis 0.099 0.008 7 Pre-2005
Lycaon pictus Lycaon_pictus -0.005 0.009 8 Pre-2005
Colobus guereza Colobus_guereza 0.243 0.020 9 Pre-2005
Callithrix jacchus Callithrix_jacchus -0.068 0.013 10 Post-2005
Pithecia pithecia Pithecia_pithecia 0.584 0.184 11 Post-2005
Varecia variegata Varecia_variegata 0.077 0.028 12 Post-2005
Lemur catta Lemur_catta 0.291 0.134 13 Post-2005
Aonyx cinereus Aonyx_cinerea 0.319 0.011 14 Post-2005
Giraffa camelopardalis Giraffa_camelopardalis 0.104 0.129 15 Post-2005
Suricata suricatta Suricata_suricatta 0.179 0.003 16 Post-2005
Macaca silenus Macaca_silenus 0.172 0.329 17 Post-2005
Callimico goeldii Callimico_goeldii -0.007 0.040 18 Post-2005
Macaca fuscata Macaca_fuscata -0.077 0.208 19 Post-2005
Leontopithecus chrysomelas Leontopithecus_chrysomelas 0.207 0.047 20 Post-2005
Panthera leo Panthera_leo 0.210 0.006 21 Post-2005
Canis lupus Canis_lupus -0.053 0.010 22 Post-2005
Papio hamadryas Papio_hamadryas 0.388 0.102 23 Post-2005
Colobus guereza Colobus_guereza 1.099 0.187 24 Post-2005
Pan troglodytes Pan_troglodytes 0.145 0.008 25 Post-2005
Alouatta caraya Alouatta_caraya 0.310 0.384 26 Post-2005
Lycaon pictus Lycaon_pictus 0.071 0.013 27 Post-2005
Macaca sylvanus Macaca_sylvanus 0.284 0.063 28 Post-2005
Leontopithecus rosalia Leontopithecus_rosalia 0.244 0.039 29 Post-2005
Saimiri sciureus Saimiri_sciureus 0.208 0.024 30 Post-2005
Saguinus imperator Saguinus_imperator 0.139 0.021 31 Post-2005
Pongo pygmaeus Pongo_pygmaeus -0.230 0.476 32 Post-2005
Callithrix geoffroyi Callithrix_geoffroyi -0.203 0.032 33 Post-2005
Panthera tigris Panthera_tigris 0.159 0.010 34 Post-2005
Gorilla gorilla Gorilla_gorilla 0.282 0.561 35 Post-2005
Octodon degus Octodon_degus 0.207 0.008 36 Post-2005
Potamochoerus porcus Potamochoerus_porcus 0.020 0.013 37 Post-2005
Lynx lynx Lynx_lynx -0.071 0.049 38 Post-2005
Saguinus bicolor Saguinus_bicolor 0.494 0.109 39 Post-2005
Cebuella pygmaea Cebuella_pygmaea 0.164 0.030 40 Post-2005
Sapajus xanthosternos Sapajus_xanthosternos 0.218 0.304 41 Post-2005
Mustela putorius Mustela_putorius -0.203 0.011 42 Post-2005
Tapirus terrestris Tapirus_terrestris 0.101 0.141 43 Post-2005
Trachypithecus cristatus Trachypithecus_cristatus 0.330 0.323 44 Post-2005
Macaca fascicularis Macaca_fascicularis -0.410 0.242 45 Post-2005
Varecia rubra Varecia_rubra 0.331 0.234 46 Post-2005
Pteropus rodricensis Pteropus_rodricensis 0.397 0.059 47 Post-2005
Saguinus oedipus Saguinus_oedipus 0.296 0.014 48 Post-2005
Symphalangus syndactylus Symphalangus_syndactylus 0.316 0.620 49 Post-2005
Ailurus fulgens Ailurus_fulgens -0.120 0.013 50 Post-2005
Phacochoerus africanus Phacochoerus_africanus 0.121 0.013 51 Post-2005
Hydrochoerus hydrochaeris Hydrochoerus_hydrochaeris -0.035 0.013 52 Post-2005
Petrogale xanthopus Petrogale_xanthopus -0.040 0.013 53 Post-2005
Nasua nasua Nasua_nasua 0.125 0.009 54 Post-2005

3 Analysis set 1: contraceptive vs. normal

Code
# variance-covariance matrix for sampling error assuming 0.5 correlation
VCV <- vcalc(vi, species, rho = 0.5, data = dat_all)


mod_all <- rma.mv(yi, V = VCV,
                     random = list(
                       ~1|species,
                       ~1|phylogeny,
                       ~1|obs_id),
                     R = list(phylogeny = cor_tree),
                     data = dat_all)
summary(mod_all)

Multivariate Meta-Analysis Model (k = 254; method: REML)

  logLik  Deviance       AIC       BIC      AICc   
 28.1053  -56.2106  -48.2106  -34.0771  -48.0493   

Variance Components:

            estim    sqrt  nlvls  fixed     factor    R 
sigma^2.1  0.0008  0.0289    169     no    species   no 
sigma^2.2  0.0186  0.1365    169     no  phylogeny  yes 
sigma^2.3  0.0228  0.1509    254     no     obs_id   no 

Model Results:

estimate      se    zval    pval   ci.lb   ci.ub     
  0.2111  0.0817  2.5826  0.0098  0.0509  0.3713  ** 

---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Code
round(i2_ml(mod_all), 2)
    I2_Total   I2_species I2_phylogeny    I2_obs_id 
       82.16         1.62        36.26        44.28 
Code
#robust(mod_all, cluster = species)  

orchard_plot(mod_all, xlab = "lnRR (all)", group = "species", g = FALSE)

Code
mod_all1 <- rma.mv(yi, V = VCV,
                   mod = ~ sex,
                  random = list(
                    ~1|species,
                    ~1|phylogeny,
                    ~1|obs_id),
                  R = list(phylogeny = cor_tree),
                  data = dat_all)
summary(mod_all1)

Multivariate Meta-Analysis Model (k = 254; method: REML)

  logLik  Deviance       AIC       BIC      AICc   
 27.5073  -55.0146  -45.0146  -27.3675  -44.7707   

Variance Components:

            estim    sqrt  nlvls  fixed     factor    R 
sigma^2.1  0.0005  0.0212    169     no    species   no 
sigma^2.2  0.0182  0.1348    169     no  phylogeny  yes 
sigma^2.3  0.0232  0.1523    254     no     obs_id   no 

Test of Moderators (coefficient 2):
QM(df = 1) = 0.3539, p-val = 0.5519

Model Results:

         estimate      se    zval    pval    ci.lb   ci.ub    
intrcpt    0.2002  0.0826  2.4236  0.0154   0.0383  0.3621  * 
sexmale    0.0140  0.0236  0.5949  0.5519  -0.0322  0.0602    

---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Code
mod_all1b <- rma.mv(yi, V = VCV,
                   mod = ~ sex - 1,
                   random = list(
                     ~1|species,
                     ~1|phylogeny,
                     ~1|obs_id),
                   R = list(phylogeny = cor_tree),
                   data = dat_all)
summary(mod_all1b)

Multivariate Meta-Analysis Model (k = 254; method: REML)

  logLik  Deviance       AIC       BIC      AICc   
 27.5073  -55.0146  -45.0146  -27.3675  -44.7707   

Variance Components:

            estim    sqrt  nlvls  fixed     factor    R 
sigma^2.1  0.0005  0.0212    169     no    species   no 
sigma^2.2  0.0182  0.1348    169     no  phylogeny  yes 
sigma^2.3  0.0232  0.1523    254     no     obs_id   no 

Test of Moderators (coefficients 1:2):
QM(df = 2) = 7.1412, p-val = 0.0281

Model Results:

           estimate      se    zval    pval   ci.lb   ci.ub     
sexfemale    0.2002  0.0826  2.4236  0.0154  0.0383  0.3621   * 
sexmale      0.2142  0.0810  2.6436  0.0082  0.0554  0.3730  ** 

---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Code
round(r2_ml(mod_all1), 2)
   R2_marginal R2_conditional 
          0.00           0.45 
Code
orchard_plot(mod_all1, mod = "sex",
             xlab = "lnRR (all)", group = "species", g = FALSE)

Code
dat_all$type <- factor(dat_all$type, 
                   levels = rev(c("surgical", "hormonal", "immunological")))

mod_all2 <- rma.mv(yi, V = VCV,
                 mod = ~ type -1,
                 random = list(
                   ~1|species,
                   ~1|phylogeny,
                   ~1|obs_id),
                 R = list(phylogeny = cor_tree),
                 data = dat_all)

summary(mod_all2)

Multivariate Meta-Analysis Model (k = 254; method: REML)

  logLik  Deviance       AIC       BIC      AICc   
 26.9339  -53.8678  -41.8678  -20.7151  -41.5235   

Variance Components:

            estim    sqrt  nlvls  fixed     factor    R 
sigma^2.1  0.0001  0.0076    169     no    species   no 
sigma^2.2  0.0190  0.1377    169     no  phylogeny  yes 
sigma^2.3  0.0235  0.1534    254     no     obs_id   no 

Test of Moderators (coefficients 1:3):
QM(df = 3) = 6.8881, p-val = 0.0756

Model Results:

                   estimate      se    zval    pval    ci.lb   ci.ub     
typeimmunological    0.2241  0.1508  1.4859  0.1373  -0.0715  0.5198     
typehormonal         0.1989  0.0851  2.3383  0.0194   0.0322  0.3656   * 
typesurgical         0.2138  0.0825  2.5907  0.0096   0.0520  0.3755  ** 

---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Code
# R^2 - hardly any
round(r2_ml(mod_all2)*100, 2)
   R2_marginal R2_conditional 
          0.12          44.79 
Code
orchard_plot(mod_all2, mod = "type",
             xlab = "lnRR (all)", group = "species", g = FALSE, angle = 90)

Code
# result table
all_models(mod_all2, mod = "type")
Fixed effect Estimate Lower CI [0.025] Upper CI [0.975] P value Lower PI [0.025] Upper PI [0.975]
Immunological 0.224 -0.072 0.520 0.137 -0.277 0.725
Hormonal 0.199 0.032 0.366 0.019 -0.238 0.636
Surgical 0.214 0.052 0.375 0.010 -0.222 0.649
Immunological-Hormonal -0.025 -0.276 0.226 0.844 -0.501 0.451
Immunological-Surgical -0.010 -0.259 0.238 0.935 -0.485 0.464
Hormonal-Surgical 0.015 -0.037 0.067 0.574 -0.393 0.422

4 Analysis set 2: sex difference

Code
# variance-covariance matrix for sampling error assuming 0.5 correlation
VCV <- vcalc(vi, species, rho = 0.5, data = dat_comb)

mod_comb <- rma.mv(yi, V = VCV,
                   mods = ~contraception - 1,
                   random = list(
                     ~1|species,
                     ~1|phylogeny,
                     ~1|obs_id),
                   R = list(phylogeny = cor_tree),
                   data = dat_comb,
                   control = list(optimizer = "Nelder-Mead"))
summary(mod_comb)

Multivariate Meta-Analysis Model (k = 242; method: REML)

  logLik  Deviance       AIC       BIC      AICc   
 19.5618  -39.1237  -25.1237   -0.8178  -24.6367   

Variance Components:

            estim    sqrt  nlvls  fixed     factor    R 
sigma^2.1  0.0000  0.0000     64     no    species   no 
sigma^2.2  0.0000  0.0001     64     no  phylogeny  yes 
sigma^2.3  0.0374  0.1934    242     no     obs_id   no 

Test of Moderators (coefficients 1:4):
QM(df = 4) = 67.2854, p-val < .0001

Model Results:

                                  estimate      se     zval    pval    ci.lb 
contraceptionF contra./M contra.    0.0902  0.0372   2.4280  0.0152   0.0174 
contraceptionF contra./M normal     0.1984  0.0335   5.9293  <.0001   0.1328 
contraceptionF normal/M contra.    -0.0855  0.0264  -3.2438  0.0012  -0.1372 
contraceptionF normal/M normal      0.0798  0.0254   3.1459  0.0017   0.0301 
                                    ci.ub      
contraceptionF contra./M contra.   0.1631    * 
contraceptionF contra./M normal    0.2640  *** 
contraceptionF normal/M contra.   -0.0339   ** 
contraceptionF normal/M normal     0.1295   ** 

---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Code
round(r2_ml(mod_comb)*100, 2)
   R2_marginal R2_conditional 
         24.01          24.01 
Code
#robust(mod_comb, cluster = species)  

orchard_plot(mod_comb, mod = "contraception",
             xlab = "log response ratio (lnRR)", group = "species", 
             g = FALSE, angle = 45)

Code
all_models(mod_comb, mod = "contraception")  
Fixed effect Estimate Lower CI [0.025] Upper CI [0.975] P value Lower PI [0.025] Upper PI [0.975]
F contra./M contra. 0.090 0.017 0.163 0.015 -0.296 0.476
F contra./M normal 0.198 0.133 0.264 0.000 -0.186 0.583
F normal/M contra. -0.086 -0.137 -0.034 0.001 -0.468 0.297
F normal/M normal 0.080 0.030 0.129 0.002 -0.302 0.462
F contra./M contra.-F contra./M normal 0.108 0.026 0.191 0.010 -0.280 0.496
F contra./M contra.-F normal/M contra. -0.176 -0.258 -0.093 0.000 -0.564 0.212
F contra./M contra.-F normal/M normal -0.010 -0.093 0.072 0.804 -0.398 0.377
F contra./M normal-F normal/M contra. -0.284 -0.355 -0.213 0.000 -0.670 0.102
F contra./M normal-F normal/M normal -0.119 -0.192 -0.045 0.002 -0.505 0.267
F normal/M contra.-F normal/M normal 0.165 0.098 0.233 0.000 -0.220 0.550
Code
# variance-covariance matrix for sampling error assuming 0.5 correlation
VCVa <- vcalc(abs_vi, species, rho = 0.5, data = dat_comb)

mod_comb_a <- rma.mv(abs_yi, V = VCVa,
                     mods = ~contraception - 1,
                     random = list(
                       ~1|species,
                       ~1|phylogeny,
                       ~1|obs_id),
                     R = list(phylogeny = cor_tree),
                     data = dat_comb,
                     control = list(optimizer = "Nelder-Mead"))
summary(mod_comb_a)

Multivariate Meta-Analysis Model (k = 242; method: REML)

   logLik   Deviance        AIC        BIC       AICc   
 132.0109  -264.0219  -250.0219  -225.7160  -249.5349   

Variance Components:

            estim    sqrt  nlvls  fixed     factor    R 
sigma^2.1  0.0000  0.0000     64     no    species   no 
sigma^2.2  0.0121  0.1098     64     no  phylogeny  yes 
sigma^2.3  0.0120  0.1097    242     no     obs_id   no 

Test of Moderators (coefficients 1:4):
QM(df = 4) = 28.1332, p-val < .0001

Model Results:

                                  estimate      se    zval    pval   ci.lb 
contraceptionF contra./M contra.    0.1731  0.0731  2.3692  0.0178  0.0299 
contraceptionF contra./M normal     0.2605  0.0727  3.5838  0.0003  0.1180 
contraceptionF normal/M contra.     0.1901  0.0707  2.6879  0.0072  0.0515 
contraceptionF normal/M normal      0.1665  0.0706  2.3576  0.0184  0.0281 
                                   ci.ub      
contraceptionF contra./M contra.  0.3164    * 
contraceptionF contra./M normal   0.4030  *** 
contraceptionF normal/M contra.   0.3286   ** 
contraceptionF normal/M normal    0.3050    * 

---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Code
round(r2_ml(mod_comb_a)*100, 2)
   R2_marginal R2_conditional 
          6.23          53.16 
Code
#robust(mod_comb_a, cluster = species)  

orchard_plot(mod_comb_a, mod = "contraception",
             xlab = "absolute log response ratio (lnRR)", group = "species", 
             g = FALSE, angle = 45)

Code
all_models(mod_comb_a, mod = "contraception", type = "abs")
Fixed effect Estimate Lower CI [0.025] Upper CI [0.975] P value Lower PI [0.025] Upper PI [0.975]
F contra./M contra. 0.173 0.030 0.316 0.018 -0.163 0.509
F contra./M normal 0.260 0.118 0.403 0.000 -0.075 0.596
F normal/M contra. 0.190 0.051 0.329 0.007 -0.144 0.524
F normal/M normal 0.167 0.028 0.305 0.018 -0.168 0.501
F contra./M contra.-F contra./M normal 0.087 0.040 0.135 0.000 -0.221 0.395
F contra./M contra.-F normal/M contra. 0.017 -0.031 0.065 0.489 -0.291 0.325
F contra./M contra.-F normal/M normal -0.007 -0.055 0.042 0.789 -0.315 0.301
F contra./M normal-F normal/M contra. -0.070 -0.112 -0.029 0.001 -0.378 0.237
F contra./M normal-F normal/M normal -0.094 -0.138 -0.050 0.000 -0.401 0.213
F normal/M contra.-F normal/M normal -0.024 -0.062 0.015 0.231 -0.330 0.283

5 Sensitivity analysis: pre- and post-2005

Code
# variance-covariance matrix for sampling error assuming 0.5 correlation
VCV <- vcalc(vi, species, rho = 0.5, data = dat_pre_post)

# 
mod_pp <- rma.mv(yi, V = VCV,
                   mod = ~ timing,
                  random = list(
                    ~1|species,
                    ~1|phylogeny,
                    ~1|obs_id),
                  R = list(phylogeny = cor_tree),
                  data = dat_pre_post)
summary(mod_pp)

Multivariate Meta-Analysis Model (k = 54; method: REML)

  logLik  Deviance       AIC       BIC      AICc   
  5.2503  -10.5006   -0.5006    9.2556    0.8037   

Variance Components:

            estim    sqrt  nlvls  fixed     factor    R 
sigma^2.1  0.0000  0.0000     46     no    species   no 
sigma^2.2  0.0017  0.0409     46     no  phylogeny  yes 
sigma^2.3  0.0144  0.1200     54     no     obs_id   no 

Test of Moderators (coefficient 2):
QM(df = 1) = 0.4661, p-val = 0.4948

Model Results:

                estimate      se     zval    pval    ci.lb   ci.ub    
intrcpt           0.1093  0.0440   2.4864  0.0129   0.0231  0.1954  * 
timingPre-2005   -0.0348  0.0510  -0.6827  0.4948  -0.1347  0.0651    

---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Code
mod_ppb <- rma.mv(yi, V = VCV,
                   mod = ~ timing - 1,
                   random = list(
                     ~1|species,
                     ~1|phylogeny,
                     ~1|obs_id),
                   R = list(phylogeny = cor_tree),
                   data = dat_pre_post)
summary(mod_ppb)

Multivariate Meta-Analysis Model (k = 54; method: REML)

  logLik  Deviance       AIC       BIC      AICc   
  5.2503  -10.5006   -0.5006    9.2556    0.8037   

Variance Components:

            estim    sqrt  nlvls  fixed     factor    R 
sigma^2.1  0.0000  0.0000     46     no    species   no 
sigma^2.2  0.0017  0.0409     46     no  phylogeny  yes 
sigma^2.3  0.0144  0.1200     54     no     obs_id   no 

Test of Moderators (coefficients 1:2):
QM(df = 2) = 6.1913, p-val = 0.0452

Model Results:

                 estimate      se    zval    pval    ci.lb   ci.ub    
timingPost-2005    0.1093  0.0440  2.4864  0.0129   0.0231  0.1954  * 
timingPre-2005     0.0745  0.0560  1.3303  0.1834  -0.0353  0.1842    

---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Code
round(r2_ml(mod_pp), 2)
   R2_marginal R2_conditional 
          0.01           0.11 
Code
orchard_plot(mod_ppb, mod = "timing",
             xlab = "lnRR (all)", group = "species", g = FALSE)

7 R Session Informtion

Code
# pander for making it look nicer
sessionInfo() %>% pander()

R version 4.3.1 (2023-06-16)

Platform: aarch64-apple-darwin20 (64-bit)

locale: en_US.UTF-8||en_US.UTF-8||en_US.UTF-8||C||en_US.UTF-8||en_US.UTF-8

attached base packages: grid, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: ggtree(v.3.8.2), ggstance(v.0.3.6), ggimage(v.0.3.3), apextra(v.0.0.0.1), cowplot(v.1.1.1), png(v.0.1-8), clubSandwich(v.0.5.10), emmeans(v.1.8.8), orchaRd(v.2.0), rotl(v.3.1.0), readxl(v.1.4.3), lme4(v.1.1-34), patchwork(v.1.1.3), kableExtra(v.1.3.4), here(v.1.0.1), ape(v.5.7-1), knitr(v.1.43), pander(v.0.6.5), metafor(v.4.2-0), numDeriv(v.2016.8-1.1), metadat(v.1.2-0), Matrix(v.1.6-1), lubridate(v.1.9.2), forcats(v.1.0.0), stringr(v.1.5.0), dplyr(v.1.1.3), purrr(v.1.0.2), readr(v.2.1.4), tidyr(v.1.3.0), tibble(v.3.2.1), ggplot2(v.3.4.3) and tidyverse(v.2.0.0)

loaded via a namespace (and not attached): sandwich(v.3.0-2), rlang(v.1.1.1), magrittr(v.2.0.3), multcomp(v.1.4-25), compiler(v.4.3.1), systemfonts(v.1.0.4), vctrs(v.0.6.3), rvest(v.1.0.3), pkgconfig(v.2.0.3), crayon(v.1.5.2), fastmap(v.1.1.1), magick(v.2.7.5), labeling(v.0.4.3), utf8(v.1.2.3), rmarkdown(v.2.24), tzdb(v.0.4.0), ggbeeswarm(v.0.7.2), nloptr(v.2.0.3), bit(v.4.0.5), xfun(v.0.40), cachem(v.1.0.8), aplot(v.0.2.0), jsonlite(v.1.8.7), progress(v.1.2.2), highr(v.0.10), parallel(v.4.3.1), prettyunits(v.1.1.1), R6(v.2.5.1), stringi(v.1.7.12), boot(v.1.3-28.1), cellranger(v.1.1.0), estimability(v.1.4.1), Rcpp(v.1.0.11), zoo(v.1.8-12), pacman(v.0.5.1), rentrez(v.1.2.3), splines(v.4.3.1), timechange(v.0.2.0), tidyselect(v.1.2.0), rstudioapi(v.0.15.0), yaml(v.2.3.7), codetools(v.0.2-19), lattice(v.0.21-8), treeio(v.1.24.3), withr(v.2.5.0), coda(v.0.19-4), evaluate(v.0.21), gridGraphics(v.0.5-1), survival(v.3.5-7), xml2(v.1.3.5), pillar(v.1.9.0), ggfun(v.0.1.2), generics(v.0.1.3), vroom(v.1.6.3), rprojroot(v.2.0.3), mathjaxr(v.1.6-0), hms(v.1.1.3), tidytree(v.0.4.5), munsell(v.0.5.0), scales(v.1.2.1), minqa(v.1.2.5), xtable(v.1.8-4), rncl(v.0.8.7), glue(v.1.6.2), lazyeval(v.0.2.2), tools(v.4.3.1), webshot(v.0.5.5), mvtnorm(v.1.2-3), XML(v.3.99-0.14), colorspace(v.2.1-0), nlme(v.3.1-163), beeswarm(v.0.4.0), vipor(v.0.4.5), latex2exp(v.0.9.6), cli(v.3.6.1), fansi(v.1.0.4), viridisLite(v.0.4.2), svglite(v.2.1.1), gtable(v.0.3.4), yulab.utils(v.0.0.9), digest(v.0.6.33), ggplotify(v.0.1.2), TH.data(v.1.1-2), farver(v.2.1.1), htmlwidgets(v.1.6.2), memoise(v.2.0.1), htmltools(v.0.5.6), lifecycle(v.1.0.3), httr(v.1.4.7), bit64(v.4.0.5) and MASS(v.7.3-60)